Epoxy in and of it'self isn't toxic, many of us use the two part putty to attach coral to rock or to build an aquascape. And that stuff cures while in the tank. That said I would be a little hesitant to use jb weld original in the tank without talking to someone who has done it.

My guess is that you could make your bond on the outside of the skimmer and let it cure and you would have little if any tank water contact with the epoxy, unless the crack is low enough to be under the water. I would search a little more and hit up a few more forums before I made the move.