Ok, i just played a little and found an ideal way to kill them - use a taser. It seems like stunning make them stop to regenerate. And also - they are VERY vurneable to stun. 5 stuns from my taser to a shoggot made it be stunned for ~20 turns.

I stunned it 5 times, dropped a stack of birdshot and 00 shot right under him, went away for 7 tiles, lit the molovot, and threw in shoggot. It exploded and after 5 turns in raging fire it’s dead.