No, you missed my point. I wasn't talking specifically about the SGA contracts, just the general issue of using established characters.
Many shows (Trek and the others I mentioned) have used cross-over characters. If Trek had wanted to use Thomas Riker, or Picard, or Troi more often, I don't think they'd have cared too much about paying the SGA salary that was required if they felt the choice of character was necessary. They seem to have just made an artistic choice to limit the use of characters in cross-overs.
The only rights-based issue I ever heard discussed was the Locarno/Paris situation, where for all intents and purposes the characters were almost identical, yet they went for a different name, even though they used the same actor. Whether that was a rights choice (not wanting to pay the creator of the Locarno character for his use) or an artistic choice (they felt Locarno was a douche and beyond redeeming) I don't know.
Doctor Who has a rights issue thing where creators of various monsters have to be credited and/or compensated for their use if they turn up in the show at a later date (Daleks and Cybermen being the prime examples). I don't know if the issue is similar in Hollywood, only knowing the examples that Fox fought tooth and nail to try to not have any acknowledgement of HR Giger in Alien 3, and had to pay Micheal Biehn a shedload of money to simply use his image in the movie.
I've as of yet never heard anything that would indicate they dropped a cross-over idea as it would have meant paying the cross-over actor too much, but of course that may have also happened, and it's practical - why use Picard when you can use Admiral Ross and do the same job cheaper, with a guest star who has been specifically picked for the recurring role?