I am 5'1" and I ride 2 Specialized road bikes (44cm) with 700cc wheels (2004 Dolce Elite and the new Ruby Expert) and I also ride a QR tri bike (46cm) which has 650cc wheels. I really prefer the 700cc wheels - mainly because it's a lot easier to find tires that I like available in stores, as well as tube availability. Also, rarely do the 650cc tires or tubes go on sale, whereas it seems you can usually find the 700cc tires and tubes on sale - at least in my experience. As far as handling, etc. - I don't see too much difference - possibly the 650cc makes for a little harsher of a ride? But I'm comparing 2 different types of bikes so it's kind of hard to tell since I've never ridden a 650cc road bike.

Also, I ride my road bike with a group of guys most of the time, and I'm more comfortable knowing that if I flat more times than I have tubes, that I'm covered by one of their spare 700cc tubes!

If the only thing that's stopping you from buying the bike is the wheel size - but you love the bike and it feels great, then I say go for it and buy it. Good luck in your decision!