Run the sport? I thought you said ruin the sport. Actually, that's what I think is happening.
The prices on the championship game have started to fall. StubHub and other resellers have had to drop their prices significantly. Football is King in Dixie, but there's much less interest in the Bay Area.
If the dominance of two, maybe three, teams continues, people will start to lose interest. People will not want to watch Bama and Clemson take everything. The other colleges and maybe even ESPN will feel pressure to in turn press the NCAA to start looking into the unfair advantages possessed by these teams. That might even include looking into cheating and bags.
This monopoly by two, really one, team will threaten interest in college football throughout the country.