The problem is that they're both portrayed as highly career-focused, and their careers are in different galaxies. So they're always going to have to choose between SG-1/Atlantis and physically being with each other. That makes it tough, unless you go AU and even then, it's hard to write AUs without SG-1 and Atlantis. The best I can come up with for genuine, untarnished happiness is set it in the future, when they've had their time with SG-1 and/or Atlantis, and are content to do something new that lets them be together. (DADT is a problem too, of course, but it's easy enough to write that away.)