Sounds like you may have a bit of a quandary..... It sounds like the shop could not put the seat post up any further on the smaller bike (there is an upper height limit having to do with the amount of post still in the seat tube), but you have a bit of a reach problem with the larger bike....

Being stretched out is never that great - you have less control and less power on the bike. If you can avoid trying to adapt a bike that is too long you'd probably be better off, but you certainly cannot put the seat post up too far - that's plain dangerous. I'm actually wondering if you might want to look into a smaller frame with non-compact geometry bike? Then there'd be less seat post out, but a shorter top tube. If I were you, I'd try looking at a 50cm non-wsd Trek 2.1 - I think it might solve your problem. The seat tube is longer and though the top tube is a bit longer too, it is not as long as the 52 wsd.