How can I interrupt auto-end-turn?

As a wise person (computer) once said

"The only way to win is not to play"

There isn't any way to reliably interrupt auto end turn, so I quickly learned to start playing without it. Its simple enough to end the turn manually, especially with the force end turn hotkey (Shift+Enter).

You can also leave one unit without any automated orders so that they always provide a stopping point, but you can quickly pass their turn to trigger the auto-end. This is dangerous though, if you forget and lose this unit or tell it to march to the other side of the world, you're back to not being able to interrupt turns.

I don't believe a hotkey for that is implemented. You could hit Control+O to get into the Options, and change it there. I think that's pretty much the fastest option in Civilization...