wooo! welcome aboard snigel! now's actually a great time to start asking questions and getting involved on SDN, because the more people hear from you early on, the more helpful they are when you're really in a pinch during the application process!
Just categorize your research experience on your applications under vet experience (there's only 3 categories: vet experience, animal experience, and non-animal related work experience). as long as it
involved animals and you were
supervised by a health professional. Some individual schools might decide not to count your research experience as vet experience, but that's their decision to make and not for you to worry about.
There's a bunch of people here who've done the research thing in all different shapes and sizes (honors theses, summer undergrad research, MS, and even PhD), so if you're worried about anything research related there's always someone here who can answer.
Like you, I work at a big hospital in Boston (as does theEVILshoe)! I pretty much said in my application/interviews that I took 2 years off after undergrad to work as a research technician just to make sure that I wasn't meant for a PhD. I didn't say much about my research in my PS though, since that's not really what my PS was about but I did put in there that because of my scientific training I would be a great asset to my field of interest (shelter med). When you write the descriptions for your experience though, I was told at least from Tufts that they want to see actual job descriptions rather than a long description on what your lab is studying. So I put a very short one liner about the topic we study, and then make a big long list of experiments i do.
I wouldn't worry too much about
working in a lab geared towards human medicine. I mean, you wanted to gain research experience, and Boston happens to be a hub for biomedical research so you took a job in a lab. Unless your lab is very clinically oriented, what you learn in your lab is probably very applicable to any biomedical research. Especially if you're employed as a technician/assistant in a lab, it's not like you picked your research topic either.
I was never asked why not MD/PhD. However, after talking very passionately about my research, I was asked by one of my interviewers "wow, you seem so passionate about your work. are you sure you want to give that up?"
(My super honest answer would have been... I'm one of those people who gets passionate about anything, like, i would be a passionate pooper scooper if that was my job... and no, i would shoot myself with the thought of pursuing a PhD... but I didn't say that). Other interviewers were just simply fascinated, and didn't question anything.
. I've had 0 contact with veterinarians outside of the shelter environment. Even then, I was only outright rejected by 1 out of the 7 schools I applied to. So if research is something you want to try, but you're finding more opportunities with MDs or PhDs, don't let that necessarily discourage you. 
