I'd say Yoren is - well, was - the closest thing to a parent for Arya, if she's emotionally invested in Gendry by now that must be for a completely different reason IMO.
She's 11. She grew up with TWO parents, plus Septas, Maesters, Nan, and of course what amounted to three big brothers--Jon Snow, Robb Stark, and Theon Greyjoy. Now there are NO adults looking out for her, except for Gendry.
Certainly she related to Yoren as a father figure in the wake of Ned's death, and related to Gendry as if he were Robb or Jon. Now Yoren's dead, too. That makes Gendry even more important. It's not necessary for her to have a crush on Gendry, for him to be the most important person in her world right now.
Just because someone's a tomboy doesn't mean she's into girls sexually. So far she shows no signs of being into anyone sexually. In fact from outward signs it doesn't look like puberty has hit her or her actress. The butcher's boy was just a friend and Gendry, at this point at least, I think is just a big brother substitute.
Well, puberty has certainly hit the actress--she has budding breasts which ruin the illusion of her being a boy at all, even though they're not large or anything. But puberty definitely hasn't hit Arya.
Personally, I think the show would have to do a lot better than that in order to convince me Arya "doesn't like boys", same as it took Ser Loras and two seasons in order to convince me Renly does like boys.
Wow--most people got it when Baelisch asked Renly "when will you be HAVING your friend?" with a nod to gorgeous Loras, who looked right past the beautiful Sansa Stark to flirt with Renly.
Be that as it may, the show shouldn't have to convince anyone that Arya is a lesbian, for us to accept that her feelings towards boys so far have been those of a little sister or a friend. She doesn't have to like girls, to be disinterested in boys. She's 11.
If Arya had a crush on anyone, she'd be rehearsing her first kiss with them in her head before sleeping, not chanting the list of people she plans to kill when she grows up over and over.