It depends on your definition of "properly," since SMW coincidentally also has a massive shortcut (the Star Road) that lets you beat the game very quickly without bending the Matrix. A TAS of such a playthrough is only 10 minutes.
There's also a TAS of 100% completion playthrough of SMW's 96 exits, which takes considerably longer. (about 1.5 hours)
This isn't about beating the game in 3 minutes. It's about exploiting a bug. Not just fiddling with code either, but actually doing it through the game itself. That's what makes it really interesting to see.
It's the difference between a baseball game and a home-run derby. Nobody's complaining that home-run derby is "cheating" because all the pitches are ideal. It's a different game altogether.
The tool-assisted speedrun people are simply playing a different game.
A better analogy would be a guy taking a taxi 26.2 miles and you coming along and saying, "I hate it when people move a marathon distance by any mode except running" for no discernable reason.
Without any offense intended, this article is basically canonical Hacker News; if you see fit to complain about it, you may not enjoy your stay here.