Why wouldn't you reward the top seeds? Again, the MAC is the only conference - to my knowledge- that doesn't reward the #1 seed at all. Right now, the only thing that matters in the MAC regular season is finishing top 8. If a conference wants to make the regular season matter more and reward teams for playing well in the regular season, you should absolutely build your tournament that way.
My preferred option would be to take the top 6 teams and give 1/2 a first round bye. It's not as extreme as the double-bye, but it makes earning the 1 or 2 valuable.
Thursday
5 PM - #3 vs #6
7:30 PM - #4 vs #5
Friday
5 PM - 4/5 winner vs #1
7:30 PM - 3/6 winner vs #2
Saturday
7:30 - Championship