Hmm, I know this is a really old thread, but this is an interesting question! Fair warning, this is going to be seriously geeky.
On the one hand, it is entirely possible that imprinting is so drastic that it could override any other dispositions a person might possess, including sexual preference. Early experiments into the real-world phenomenon of filial imprinting discovered that young birds could be made to imprint upon humans, and even inanimate objects such as white balls, as they would their natural mothers. (For a very famous example, search for "Lorenz's geese".)
However, it is extremely ambiguous what actually triggers an imprint. Given that shape-shifters have a heightened sense of smell, it is possible that olfactory cues, perhaps even pheromones, are involved. Research has indicated that there are differences in how gay or straight people respond to certain odours, with gay people responding similarly to straight members of the opposite sex. In this case, it is quite plausible that gay werewolves will generally imprint upon members of the same sex. Whether they would imprint upon a gay member of the same sex remains up for debate, although one rather hopes for both their sakes that they would. Since the actual role of the imprinter appear to be determined by the needs of the imprintee, perhaps the relationship would be chaste as we see with very young imprintees.
More broadly, homosexuality is a natural phenotype in humans and many other animals that appears to have some genetic basis, so unless there is some powerful negative selection (e.g. werewolves not imprinting upon humans whose children might have a genetic predisposition towards homosexuality) or other genetic imperative going on, it is reasonable to assume that there will be gay werewolves. Since imprinting seems to have some function in introducing positive characteristics into the pack, such werewolves could be seen as providing beneficial influences beyond the merely genetic, thus indirectly improving the pack's position in a manner similar to kin selection. (Which, in itself, may contribute to the existence of homosexuality in general, the so-called "gay uncle hypothesis".)
So to summarise, while it's entirely possible that a gay werewolf might imprint upon a member of the opposite sex, it seems perfectly consistent and harmonious—in more ways than one!—for them to imprint upon a (hopefully gay) member of the same sex.