It should be fine as long as you don’t turn it into porn, I guess 
The best approach would be a FE Holy War approach (remember how there was actual incest in there too, specially with the Claude x Sylvia pairing?). It’s not like the series haven’t had stuff like this before and putting a taboo thematic there would give A LOT of spice to any plot, specially if you somehow put a debate ingame.
Example of Seliph and Yulia: they obviously like each other from the beggining and, even though the game doesn’t explore this relationship, it’s clear what the intentions of the devs were, specially because you can pair them by using glitches, which means it was programmed into the game. This is better explored in the manga.
Same with the example of Eldigan and Raquesis/Laquesis.
Last but no least: FEU Content Policy - Fire Emblem Universe (feuniverse.us)
So yeah, you should be fine as long as you don’t make any explicit scenes.
Edit: by the way, which is your hack? Is there a public beta already?