Shephard didn't die at the end of OpFor. He was detained. Speculation is that since the Gman already had Gordon, he didn't need another dude, but as explained in his ending speech he didn't want to see Shephards potential go to waste. So the speculation is that the Gman is keeping him as a "backup", in case Gordon fails or something.
As for all the "Gman is Gordon", "Gman is Gordon's father", "Gman is Gordon from another dimension", "Gman is Gordon's step-uncle's second cousin twice removed" or what have you theories, the only evidence to support it is that they look slightly similar (and honestly, I don't see it myself)
There's also the issue of Gordon never speaking. That's kinda been one of the main gimmicks of the HL series in that the main character never speaks. If the Gman were Gordon, and you obviously hear the Gman speak quite a bit, it would just be weird.
Personally I don't think we'll ever really know who or what the Gman is. I have my own theories, but I wouldn't be surprised if valve never told us for sure.
Moo.