I ride both 650 and 700c wheels, and am 5'1". My Cervelo P3 (size 48) has 650s, my Specialized Ruby and Dolce (size 44) have 700s. I agree with others that it's an easy acceleration on the 650s, more so than on the 700s, but I also wonder if that's a function of gearing as well. I think you won't be disappointed going either way. Have you tried them both out? Also, like others have mentioned, for the 650s you're more limited in wheels and tires, and make sure you have spare tubes with you b/c it's more than likely that others will be riding 700s.

Sorry I don't have better advice. Go with your gut feeling - you won't be disappointed in the 650s if that size bike fits you better. Good luck!