I don't see how Djokovic goes above Fed on clay automatically if wins 2 RG titles. It's quite evident that if Nadal comes back even close to what he was Djokovic is unlikely to beat him, although I still maintain he has a better shot than Federer ever did. If he comes back, and he's not half as good as what he was, that would just mean that Djokovic bagged 2 RG titles in a "weak" clay era (for lack of a better word). The only difference between them then would be that Djokovic didn't have to play Nadal twice in the final, and Federer got "lucky" only once.
I hate to bring this up because it's very hypothetical, but I think without Nadal, Federer has at least 3 RG titles, and IMHO that's the only way Djokovic is getting 2. He had enough trouble with Seppi and Tsonga this year for gods sake, and he lost a set to Delpo in 2011 when he was only in the process of coming back. Delpo has pushed Federer hard there twice now, he could certainly do the same to Novak, and if he gets that close who's to say he won't beat him.
Nadal is getting older, but so is Djokovic, which means he's more likely to get upset. Say Djokovic makes the final the next two years. He'll be 26 this coming year, and 27 the next. Will he make the final again at 28 and beyond with his style of play even if the next generation is supposedly weak. I'm not so sure. If he does, all power to him, but given this scenario which I think is relatively likely he'll have to cash in 2 for 2 the next 2 years. I think he'll win at least 1 RG for the record. Now I could be totally wrong obviously, but these are just my thoughts.