My second play through with another character, I decided they all had to die (but I let Mobius live. Someone has to mind Big Mt while I'm away.)
I discovered that if you don't talk to them when you go in (after the scripting warns you that you'll be confronting Dr. Klein now) they will still be friendly towards you and willow allow you to drop C-4 and pulse mines near them. Then when you confront Dr. Klein, they go hostile, but you can detonate the C-4 - which also sets off the pulse mines - and then finish them off with the sonic emitter. It was pretty sweet doing that. Teach them not to put their cybernetic mits on my brain, heart, and spine!