I just fast traveled there for the first time in forever and noticed Hancock dead just outside where those mutants are always holed up (between hangman's alley and diamond city). I went back 4 days worth of saves and noticed he's been lying dead forever and I'm not gonna erase all of that progress to save him.
Just about everytime I go to that settlement the settlers run off and engage those damn super mutants, so my advice to everyone (if this hasn't already been said a million times) is to NEVER leave a companion at that place or any other place that is holed up directly next to AI spawns. Otherwise you could travel there and build stuff and have one of them run off without you even knowing it and get killed.