But because we are not voting for the game it self, but to a well-made, fast and entertaining run, I'll give this a Yes vote.
Hmm... I just noticed that this run was already accepted but i guess saying out loud my oppinions isn't a bad thing. :)
This isn't a criticism on the performance of the author so much as the fact that a 100% run is just not entertaining. The hack doesn't really introduce anything new to the game beyond a different map, nor is the map design inspired or new enough to make the different level design interesting for a TAS. 90 minutes is a long time to be sitting watching any individual speedrun, especially speedruns which do not significantly vary from existing runs (the regular Super Metroid runs on the site were actually more interesting because I was unfamiliar with the tricks associated and seeing them used in familiar places to do unfamiliar things made the runs interesting. Seeing them used again in unfamiliar places is not as novel).
The TAS of the hack must show something not seen before in the TAS of the original game (for example, doing some good looking move that is infeasible in the TAS of the original game timewise, but made mandatory in the hack)
The pacifist idea is very good in Contra games because of the insane amount of enemies in the screen.
At first I doubted that this would make an interesting run, I was wrong. Voting yes.
But the game isn't really finished no matter where I stop it, so I figured it doesn't really matter. And stopping it right after the final blow is always the most impressive way to do it.
Sorry for the late submission!