That sort of thing happens, and it generally happens in such a way that there's no huge problems brought up either regarding internal consistency or bad out of game implications. Generally.
There is one glaring exception.
It has to do with the rights of non-straight people.
The queen-to-be dancing with another woman is considered scandalous. If you tell the game that you want to marry another woman the best you can pull off is making her your lady in waiting, having both of you marry other people, and then having sexy-fun-times when no one is looking.
Same sex relationships, male and female, are kept hidden.
And, for the nobility, since titles are hereditary it's absolutely vital for stability (read: not-civil-war), that they marry members of the opposite sex and have kids.
All of that implies a less than good situation for people attracted to members of the same sex.
There is something you can do to change all that. But before I get to it, some background.
Lumens are magic users. They get their magic from special crystals that they bond with for life. (Want another Lumen's crystal? You've got to kill them.) They are generally regarded with fear. Possibly hate. A while back court politics went less than well and, since the ruling class was composed entirely of Lumens, magic was used, things went to shit, after the fallout there would only be two open Lumens until the time of the game, all the others either gave up their power or said they did.
One was whoever the current ruler of the kingdom was. It was acknowledged that some problems needed magic to fix, rulers can get away with shit, so a Lumen crystal was passed down through the royal line.
The other was the family line of your first option in magic teacher. They've been hated and feared for hundreds of years because they felt it was necessary to keep magic alive and not lose the knowledge thereof.
Background point two.
You will be invaded. It cannot be stopped. I'll talk about that when I get to inconsistency because there's really some evidence based on the handling of past events that it should have been stoppable.
There are several ways to deal with this, but the pertinent two go like this:
Your navy gets its butt kicked meaning lots of people die and your military is generally fucked. Surviving soldiers sacrifice their lives to buy time even though, well, that's pointless. Then it turns out that what the enemy king is really after is your Lumen crystal, so he wants to duel with you and win or lose he'll call off the invasion.
At this point the two important-to-us options come up.
1 You can use high skills involved in conversational manipulation and just plain being an imposing force worth listening to combined with personal knowledge of the enemy king and an ability to be a kickass heart string tugging musician to redeem him and have him go home in peace. Other than death and turning evil, this is the only option in the entire game that does not leave your kingdom under the constant burden of knowing that the country in question wants to retaliate.
2 You can kill him in a magic duel.
Background over, it is possible to have a same sex marriage in the game. Here's what you have to do:
Lose the naval battle killing off most of your military. Lose a lot of what remains in a losing battle against the invaders cutting a swath of destruction across your country.
Fight and win in the duel.
Find out that while the enemy king was completely serious about calling off the invasion it's kind of hard for him to do once he's dead. The high level commanders all return home, but many of the soldiers go AWOL, bringing lawlessness and death and whatnot to your country. Also you'll have trouble with soldiers turned bandits into the foreseeable future.
Back in foreign country the Queen is pissed off beyond all measure that you killed her husband and begins the process of regrouping so she can take revenge.
And then two women can get married.
Got that all non-straight people? You can only get married in public (the affairs going on behind the scenes are more inclusive) if you're willing to destabilize a nation and have this generation live under constant fear of retaliation.
Seriously, take notes.
Except... it's worse than that.
You see killing the enemy king in a duel is the only way you can raise the status of Lumens above an uncomfortable subject that sometimes involves produce being thrown at people. I've cheated to max out skills (thus opening basically all options) and tried every Lumen popularity related variation I can think of. There is nothing else.
But killing the enemy king doesn't just raise the status of Lumens to, "Let us treat them with respect as we would any other person," it makes them into idols. It's the highest public opinion has been in living memory.
Little kids pretend to be them and want to be them when they grow up.
In this setting your magic tutor and her lover (who can be your magic tutor if you don't accept the first) feel comfortable coming out publicly as Lumens in love and then get married, by you, the queen.
Let's break that down.
The queen gets a pass on being a Lumen because she's the queen, but her personal support isn't enough for people to not throw produce at her tutor. So her being a Lumen doesn't matter much.
The other publicly known Lumen is who all those kids playing at being Lumens can aspire to be when they grow up. While others might come forward now that there's not a need to keep it hidden (her lover does) she's the one everyone knows about. Then she gets married to another Lumen, double awesome points, and the wedding is officiated by the queen, awesome icing, and the other Lumen is also a woman.
Now children are left thinking, "I want to be like that married lesbian when I grow up." Will this turn children gay? Of course not. Will this go a long way towards establishing marriage equality in the country of Nova? Almost certainly.
But then the situation for people with same sex attraction gets better.
The couple adopts.
Showing that adoption can work as an heir producing method is absolutely vital if members of the nobility want to have same sex marriage. There are other obstacles (just dancing with a woman was scandalous when the princess did it) but in many ways the high profile lesbian couple will go a long way towards dealing with the other obstacles. What can't be dealt with is the fact that two people of the same sex cannot produce a child.
Under certain circumstances the player character will even say to someone, someone who can become her romantic partner later, that it doesn't matter if the woman doesn't like men, she needs to get married to one and produce an heir pronto. After that she can get divorced.
But if you've established that adoption is ok then suddenly that pressure evaporates. Now, admittedly, the adoption was someone with family ties (the niece of one of the women) so it doesn't overturn everything, but it goes a long way toward letting the nobility have marriage equality and what the nobility does will tend to filter down to the rest of the country.
So you get to choose between lasting peace and what seems like it would mean an explosion of equal rights and public respect for non-straight people.
And either way requires you to lose a bunch of lives by having the opposing army sink your navy and trample your lands.
That's an unfortunate implication. "Yeah, we can have gay rights, we just need to ruin the country and place it at risk of future invasion."