Ranka is bi, somewhat femme, and a drag queen, but doesn't seem to be an actual transexual iirc (i.e. Ranka doesn't identify as a woman). So, Haruhi's father is still Haruhi's father.
That said, I would think she'd celebrate both. What's the point of building a shrine to your dead relatives in your living room if you don't give it a bit of attention on the proper holidays?