I see nothing wrong with a mid-major conference protecting their top 2 seeds? They had the best seasons and you only get limited chances to get get at-large bids.
I like when conference champs (or higher seeds) are rewarded in mid- and low-major conferences. It rewards the regular season, it gives less of a chance that there will be a bad bid-stealer, and results in the best chance to have the best team make the tournament.
Every bubble team should root for chalk in mediocre/bad conferences that have an at-large lock program. You can argue that Gonzaga has gotten a higher seed than they deserve in the past, but it's hard to argue they weren't a deserving team to make the tournament. So, if they had lost early, it just would've taken a bid away from a bubble team.