Well, having looked at all the posts from this morning, I think my reason for sharing the story has rung true - just to let people know about this and to make sure they have a shut off switch and know where it is located. That was my intent.
Just to clarify, we do have a main shutoff for the thruster (apart from the joystick panel, which only shuts off the low amp signal to the control box and solinoid on the motor). It is not the plunger type in the earlier posts - it is actually a large key turn type device (it has a handle but doesn't take a key, just don't know what it is technically called). It would have been a bit more convenient to have it right at the helm, but it is only about six steps away. Once I realized what was happening, I ran to the berth, shut it off, and returned to helm so quickly that no one realized that anything was amiss.
If it turns out the control unit is bad, Sidepower has a revised one that does have a timed shutoff, in addition to a thermal shutdown. I think the timer is around three minutes of the thruster actually running. The shutoff on the joystick switch is 10 min without any use. The three minutes, as well as thermal shutdown, would not have helped do to the tight quarters we were in. I think it is to prevent the unit from running while underway where the crew may not hear it over engine noise (I found one instance of this happening on another forum).
Again, though, the key take away is to make sure you have a shutdown, probably best if it is not tied to any other systems (except maybe the windlass), and know where it is located.