I am at a smaller program, and would pick it again. The reality about coverage is that in any program, if somebody on your block is out, your work will likely go up. In a 10-12 person program, they just have more blocks to cover. Frankly, if somebody doesn't show up for whatever reason, then the attendings are the ones that get screwed.
I don't think it is a big enough concern to make it a real factor in the decision. The things about a program that make it small (ie community vs academic, lack of fellowship competition, geographic location) and the benefits (lots more direct interaction with faculty, functioning as a fellow on the subspeciality rotations, more direct clinical experience and better case numbers) are likely the reasons you are interested in it. So, to give up what you want in a program for some remote possibility of taking 2 extra calls in a month over your residency seems foolish.