Not worth the change over since you'll need to change the PSU too.
Basically everything in the rig will hold the 560Ti from performing even at it's least.
Things that you will need to change if you choose the 560Ti would be, CPU, PSU, Mobo, RAM..... that's nearly everything.
It would be better to go for an average GPU then to invest in the 560Ti for that rig.
550 ti (assuming you want nVidia), with some PSU upgrade. You should be able to put it with some BIOS update (no guarantee) though it SHOULD, there is some cases that the BIOS doesn't support the PCI-E 2.0, so good luck .
You mean to say all games that will actually work smoothly with the Pentium D right?
Cos that will be the main factor that's going to limit games to a particular standard.
Stick to that card.... don't add any money to that rig for now, save up, and wait for a good machine making budget. Then make the best with what you have and enjoy it....