http://tasvideos.org/2027M.html
That movie has a star and not only uses the above "debug code" but also uses a code at the beginning while on "Cheat Mode" to reconfigure the layout of the levels. Interestingly, that run had no controversy about acceptance. It was faster than the existing run of the given criteria, and so it was accepted.
Why would this run be any different?
As the old adage goes, past mistakes don't justify repeating them.
(I'm not saying accepting that run was a mistake. I'm just saying that arguing that this should be accepted because that one was too is not valid. In general, runs don't set precedents.)
In that case I would argue it's worth making an exception for this run on it's own merits. As has been pointed out before, the GT Code doesn't make the game easier. It makes the run much harder and allows the creators to demonstrate more skill and even new tricks.
It does make the run shorter though. So I do think this shouldn't obsolete any%. But I don't think it should be out-right rejected as it seems to me that the run does not violate the spirit of the rule.