Although grades are certainly looked at, and their are some (many?) programs that will cross you off just b/c of them, its not the case with all. My advise is to make a list of programs with whom you can make to the time to ROTATE with -- one month each. I would recommend using every elective you have for a rotation at a new prospective program.
Face time gives you the best chance of getting an interview. If you don't interview, you've got no chance, and as you suspect, w/ lesser scores there's lesser chance of an interview w/o rotating. ROTATE, ROTATE, ROTATE.
Good Luck.