I kind of like that bug actually. If I were to be an engineer I wouldn't want to hold down 1 button constantly while running around the ship to repair everything at max speed and if furiously clicking leads to the same result then I would probably hold it down.
I honestly don't think holding down 1 button for the entire match makes the role of the engineer more fun.
The bug is kind of realistic too, if you think about it: The faster you swing your arm, the more hits per second you get.
Back to the original topic, I like the idea of this new tool, I am not sure if it doesn't need more repair power though. If you have 2 engineers and 1 of them has this tool, then you are going to lose 1-3 other vital components that you simply cannot repair, or can you? But that's a risk/reward balance issue.
Rebuilding isn't so great, so if your component dies you are kinda screwed, making a combination with a spanner would be somewhat obligatory.