The level-object-undo is a known bug.

Simple workaround solution to the level-object-undo bug: Make the red object the last object in the level's object list, so if you delete too far, you delete your red ball, and then you have to start over again.

And as I said before, I think it would be best to have some sort of scoring system that gives bonuses if you can do things like no-pause or no-delete or one-stroke-win, rather than taking those things away.