No worries about 1.0 vs 2.0 PCI-E, as they both work together and are compatible.
As for the card blocking your SATA connections, have you looked at low profile, 90 degree SATA cables?
SATA Internal Cables at CableGear
Any particular reason you want to go for a card that is now two generations behind? Yeah, they're cheaper now, but there are better cards out there for about the same money. The 9600, ATI 3870, and ATI 4850 are all better than the 8800.
Also, make sure your PSu can handle the card, whichever you choose.