There are gyms with lower capacity than some of the WCC schools that don't look like high school gyms. There were some pretty small gyms in the MWC (AFA isn't quite 6K), but they didn't look small-time like a couple of the WCC gyms. What makes St. Mary's, LMU, and Pepperdine look like a high school gym is that there's a wall behind the baskets. If you make the seats go all the way around the court, it doesn't matter as much how many total seats there are.
For an example of that, look at Santa Clara. Their capacity is only 4500, and their gym doesn't look like a high school gym. It looks like a college basketball arena. It's small, but it doesn't look small time.