I don't dislike rodents, but I did have a bit of a problem with my rodent-related research. I worked on embryonic neural stem cells, and this required me to sacrifice pregnant mice, something that my family and friends had no trouble telling me was evil. I figured, hey, they use mouse traps; if inconvenenience is reason enough to kill a mouse, why isn't the promotion of health? Anyway, I felt that the ethics of my decision to go forward with the research were logically sound, but it still felt bad/wrong. I'm the kind of person who, as a kid, wouldn't even kill insects. I eventually just got used to it, which is probably kind of horrifying in and of itself.
Anyway, to the OP: maybe it will help if you imagine they're all mickey mouse or something? The one part of my research that was difficult to stomach involved vaginal probing on mice; it was simply disgusting, but after a few mornings doing the job, I just kind of got over being grossed out. Just give it time, and try not to think about how skeeved out you are.