I have exactly the same screen setup as you. I think that having a lower FPS can only be countered by buying a better graphics card.
A GeForce 8800 or something similar should be sufficient. (a GeForce 8800GT seems to perform better than a 9600GT by the way, and the former is cheaper than the latter)
I have a GeForce 7900 with 768MB RAM and this can perform well in Windows XP 64bit. I don't use horizontal spanning, I use both screens separately.

[edit] I don't know how much of a performance loss I encounter at home with horizontal span vs. dualscreen. I just know that I get 20 to 140fps, depending on the environment, which is very acceptible.

If you have old graphics card drivers, you might want to consider updating them.