Here's a simple solution to the Staten Island controversy...the conference could award the NCAA bid to the regular season championship instead of the tournament championship.
There were two conferences (SAA and SCAC) that had tournament finals with no particular meaning. In the SAA, everyone knew Centre would get the Pool B bid no matter what Oglethorpe did. In the SCAC, Centenary wasn't eligible for the postseason, so no matter what happened in that final, Trinity was going. The games were still excellent.
I don't think there is a rule that the autobid has to go to the tournament winner, so you could still have the tournament, but Staten Island doesn't get hurt by their first bad game in three months.
While there is no rule that says you have to give your bid to your conference tournament champion, you do have to give the bid to your tournament champion if you want to have the conference tournament games exempt from your 25 total games. So you can do that but teams can only play 22 or 23 games during the year if they want to participate in the conference tournament (Bylaw 22.214.171.124.1.1.b)
(SAA must have gotten a waiver while they were serving their two years)