I hope you are not too bored for me commenting on this again.

So, I have re-though about this issue today and decided to solve it
differently (and will include a patch here this time, don't worry about
mentions to external repo this time).
To solve the problem I replaced the tk.call method in the Tk so it can
remove registered commands in the call in case it fails. 

The other problems reported in this issue are also solved by it, and
others that weren't reported are too: Misc.selection_handle (just to
name one, but there are others) could leave a undesired item in
_tclCommands too.

Another advantage of this solution is that extensions benefit from it,
and they do not need to change their code (except if they are using a
collection of internal functions, which they shouldn't, affected by this
patch).