I voted "Toggle by Engineer," but I'd like both almost equally.
What I'd really like is a global setting rather than engineer or dock (anything that can be accelerated) based.
Either way, I think there should be a "global engineer autoassist disable" button (like the PAUSE ALL button, maybe a Control-click of it?) so if the resources get really negative you can slow things down easily...?
Of course, with the "Anti-Admiral patch" (parasite cap; I'm joking - hey, I had an Admiral patch some releases ago so I guess it all evens out in the end) there will be many fewer engineers on a team (at least, on one of my teams, where I usually cart around 40+ Engineer IIIs on offense and leave 8 on defense at every planet) so it is not that important one way or the other.