The Legend of Korra - Book 2: Spirits

 Spoiler

All I can think of that can save the mess korra has made is (that after some awesome fight episodes and she manages to get vaatu out of unalaq) for her to take vaatu inside her, safest place I can think of since she can't destroy vaatu without making an even bigger mess and then from now on the avatar has to manage both spirits inside of him/her.

If she can't manage to do it the worse that can happen is what 李船長 said, kill them while they are still one and good luck getting vaatu out of the next dark avatar.