You maybe have missed something..... like going back to speak to the quest giver.... if you don't get a well done or something.... you probably missed something else.
I killed everybody at the car factory I thought...... except the main target, got him later.
As far as I can tell, the "normal" way through this situation is to take him at his word, agree to plug the leaks and then restart the pump when he offers to let you do so. You have already found you get a few Mirelurks popping out of the machinery. Make sure you don't hit him as you kill them and he should comment that it will take some time to drain the quarry and he cannot reward you with anything other than a few caps. He should still be non-hostile.
As for what happens next...
There are clues that this will happen in his terminal.
This should be in the spoilers section:
What I did: read his terminals - walked up to him - shot him in the face - closed the valves - turned the pump on and ran from the mirelurks - quest was completed.