It's one thing for her to criticize the system, and altogether another to propose something better. Here are a few problems I see with her article:
1. For one thing she ignores the fact that the FCS teams cost their Universities as much, or more, than the non-AQ FBS. Forcing those schools down a rung would make them less competitive, but would not decrease their losses. Did that solve anything?
2. The real losses from a football team are not from the team itself, which does produce revenue, but rather from the fact that the Title IX requires there to be an equal number of female athletes, meaning a lot of non-revenue producing women's sports, all of which lose money.
3. Next, she ignores the fact that these "power teams" need to have someone to play. Only 14 teams have made it to the the BCS Championship game, so, let's take her example to the extreme, and have a top division that consists of only those 14 teams, and they each play a 13 game round-robin schedule. OK - you'd see some very good games, the best against the best. But, guess what - now half of those 14 teams would have a losing record ever year. Hypothetically, suppose OSU was in those 14 teams,  but had a losing record every year. Would that help or hurt fan support? Would that increase or decrease revenue? Would fans be happier, or not? Before going this way, you need to answer those questions.

If you follow her logic, perhaps the logical thing to do would be to separate the football teams from Universities, and make them into independent businesses. The ones that lose money would vanish. Without the money losing football teams, athletic departments could dramatically reduce expenses. With 125 male athletes gone, they could also eliminate offsetting women's sports, and lose an additional 125 female athletes. Sports like women's volleyball and basketball would remain, of course, as would men's basketball, but a lot of minor sports could be eliminated at a big savings.

There is actually a precedent for this change, by the way. Years ago football teams were sponsored by businesses, who, to get better, would employ "ringers". Later on the teams were spun off, and became independent. The Green Bay Packers no longer are employees of the Indian Packing company, for example, and the Bears are no longer called the Decatur Staleys after the A.E. Staley Food Company.