I'm philosophically opposed to your changing Timothy's name. Partially because it's such a complex name--connotations of plants, healing, timidity and strength--and partially because there are Timothy's out there who need a good role-model. Mostly, though, because his name is linked, in you, to his soul. That's why you're having trouble changing it. I think you absolutely shouldn't change it unless your editor insists.

I, too, dislike the name Harry. And Ron, for that matter. Ginny as a nickname for Virginia leaves me cold. And yet I DEVOURED the Harry Potter books. So, although I personally love the name Timothy, I don't think it matters if readers like it or not. The story will suck them in, and by the end, THIS will be there association with that name.