Gonzaga beats up on a bunch of weak teams in their conference every year and gets a favorable NCAA seed which allows them to usually get past the first weekend.
If Gonzaga played a Big 12 conference schedule, I guarantee their record wouldn't be nearly as glossy (e.g., this year's Cincinnati, UCF, Houston, and BYU football records) and their tournament seed wouldn't be as high.
Would they elevate an already tough Big 12 basketball conference? Yes, for the short term, but I'm not as sure about the long term. Also, admitting a non-football school into the league makes things messy.