I can almost guarantee that they wouldn't throw TGC in with the rest of season two if and when the release them. The second half of season 2 is 26 episodes long and TGC is 13 episodes. There is almost no way they'd release a set of 39 episodes. It's almost never done. Plus, like Joshua said they are two separate things. Though, with the fact that the first two dvd sets didn't sell that well if they did decide to release the rest of the series they might just want to do it in one big set to get it done and over with.
I don't hate TGC. While that season wasn't nearly as good as the first two, it had some good episodes. I'd definitely buy it if the released it (partly because I'm a completest and I'd want the whole series).