if my opponent uses mutant massacre to remove one of my stunned characters from the game, would using chaos magic to target that effect to another one of my (live) characters be negated since mutant massacre only works on a stunned character?

Nope. Need a legal target. Massacre requires a target stunned character. So you'd need a stunned character for it to target. Otherwise, the card would be amazing rather than a meta-card. And by amazing I mean about half as good as Bwa Ha Ha.

Chaos Magic can't force it onto an illegal target. So, you're either pushing Mutant Massacre onto another legal, stunned target, or leaving it on the current one.

hmm... is there anything that can stop mutant massacre??? lol... my friend has a very good x-men deck... and well... when you play against a very good deck... it can get annoying lol...

either make the character untargetable, (BPRD signal Device) or KO the character to some other effect, so the Massacre wont prevent re-recruting, or recover the character.

would that work even if the character is stunned?

BPRD Signal Device would allow you to pay endurance, I believe, to make him unable to be targetted by effects. If you know your opponent is packing Mutant Massacre, then before he stuns, pay for the effect. It will still protect him even if he's stunned.

just remember to pay the END before the Character stuns. ;)