That's not necessarily true. There were plenty of options...
#1: Stay on SG-1, appear once or a few times on Atlantis. (what actually happened)
#2: Stay on SG-1 (the team), but as a special guest star. She appears in about ten episodes. Her absences are explained away as helping the Atlantis Expedition. On Atlantis, she is paired up with McKay in a recurring role as an SGC asset sent in for problems that the McKay-Zelenka duo cannot handle on their own. I'm not sure how this would work without making McKay look #2 to Carter or reducing Zelenka's role.
#3: Carter is given command of a ship, something that eventually happened. I suspect it would be the Odyssey. I wouldn't be surprised given it's large role in Season 10 and Mitch Pileggi's (Caldwell) reduced availability.
#4: Carter's no longer affiliated with SG-1 but rather the SGC. She's simply sent where needed. This could mean helping SG-1, helping Atlantis, commanding the Odyssey, coordinating from an off world base, and so on.
There are other options, but you get the idea. It's not fair to the producers and writers to say they didn't have a clue. The simple answer: they hadn't reached a decision.