I like Carter! She had a small-town personality with near-obsession with being a professional. She wasn't a deus ex machina, she often served to show the characters their mission - what they had to do to solve the plot. She hardly ever solved things by herself, and when she did it was threw ingenuity rather than technobable. I could relate with her very much!
Atlantis didn't destroy her character. In season 4, she rescued Atlantis in deep space, oversaw construction of Midway station, was responsible for the destruction of the Asurian Replications, determined who was responsible for the Hoffian plague, and led a rescue mission when Michael's lab imploded. She was a lot more hands-on than Weir ever was, and with her scientific expertise Carter was able to see problems and find solutions that in previous years nobody would have seen until it was too late. I'd say she was responsible for rescuing Atlantis and Pegasus from many mistakes and doing so compentently. Destroy her character? No, unless you don't like the show in the first place (in which case you are transferring your distaste for the plots to the characters).