Part of me thinks they did get screwed. I actually spent part of the morning talking to my friend who's also a WKU fan about this.
On one hand, yeah, you (likely) can't go in and lose your first conference tourney game. On the other hand, MTSU was "ranked" to end the season and we always hear the committee's bull**** about how if a mid-major can prove itself in the big dance, they'll be able to get the benefit over some of the bigger teams in the future. Obviously we've seen what Middle has done in the last couple of years, including the biggest upset in tournament history (by certain metrics) and another upset win last year, and let's be honest, they were under seeded last year.
As always, no one can trust the committee, especially in the world of mid-majors. It's true that I hate Middle, but as a rational fan of a conference rival I would probably be furious if it was WKU. But on a hypothetical third and final hand, I'm not even sure beating Southern Miss would've clinched it for them since they got a friggin 3 seed in the NIT. It just seems weird that a ranked team in March would still have to win their conference tournament, especially one with a very recent history of big tourney wins.