Some schools specifically state that they do not use graduate coursework in calculating GPA, although I can't recall which ones off the top of my head.
The simple answer -
They will (all that I've spoken to and looked at) use and calculate grad course work - but they also calculate undergrad.
The only way to avoid your undergrad (not really the question I know), is to retake ALL pre-reqs as a grad student (and that only works at SOME vet schools, and its not really very realistic).
The thing about grad work are grades tend to be inflated (I was a B/C student as undergrad, 3.7 gpa (I think) as a graduate). This is for several reasons.
A) You have nothing to do except these 2-3 hard classes a semester (Advanced Biochem and Physical Biochemistry really isn't that hard when it is the only think you are taking)
B) You are expected to teach, do research, write, go to conferences, ect. - They (prof.) tend to cut you some slack in classes
C) As a grad student, you are not 1/400 other students who all want to be "Pre-Med", you are 0.1% of the students who started, you are serious about it, and MUCH more dedicated (you are also more mature then when you started), so of course your grades will be higher.
I would def. take the MS (if you really think you can pull it off in 2 years).
Its only 1 extra year
It will help you a lot when you do get into vet school
May open more doors after vet school (don't know much about AS degrees)
Its a wonderful experience (I loved my grad school life (even if I want to strangle someone now)