Like how she let Rogue stay with the X-Men, when Rogue convinced her she wasn't brainwashed?
After Rogue had had to run away from home because Mystique couldn't admit that she couldn't help her control her powers? I agree that letting her go was the right thing to do, but it's not like she left her alone after that.
And what storyline suggest this theory?
What theory? She created and led an incarnation of the Brotherhood of Evil Mutants for heavens sake, then when things looked bad for them, she turned tail and became a Government agent (Hardly speaking volumes for her committment to the cause of mutant rights, and speaking to a more pronounced sense of self-preservation). Then as soon as that went south, back to the self serving villainy.