The short answer is yes. But I wouldn't bother with the GT610 as it's so underpowered, I would either use the on-die Intel HD graphics or look at a more powerful graphics card. If it's just normal office stuff, web browsing and video playback I'd go with the on-die Intel HD, if you're looking to play games I'd be looking to a Radeon HD 7750 or GT640 as a bare minimum.
PCIe 3.0 is really only be needed by the really high-end graphics cards in the coming months and years as graphics cards get more powerful and need faster interfaces with the memory and cpu. Just now, PCIe 2.0 is capable enough for all but the most powerful graphics, even the the most powerful are only marginally held back.
In answer to this, the original Sandy Bridge processors only support upto PCIe 2.0 interfaces. When the newer Ivy Bridge motherboards came along with the faster PCIe 3.0 interfaces they needed an Ivy Bridge processor to run them as PCIe 3.0. Although the Ivy-Bridge motherboards were backward compatible and would run with Sandy Bridge processors they were restricted to PCIe 2.0 speeds on the PCIe interfaces.
However, all this is purely academical as there is nothing in the build that actually requires PCIe 3.0.
Have you considered looking at AMD FM series? I cannot speak from experience on this but the FM APUs are supposed have on-die graphics which are more powerful than Intel's, and it'll certainly be more powerful than a GT610.
Here's a Tom's article on one that they recently built, I think it'll be more powerful and cheaper (no need for a discrete graphics card).
You're fine. All PCIe interfaces, whether they be 1.0, 2.0 or 3.0 are all desgined to be backward compatible so they work at their fastest common speeds. Don't forget, we still had a lot of powerful hardware on PCIe 2.0.