Just go the Olympic route. Schools can give a scholarship, players can get endorsements. There is no reason the 2nd string kicker at LaTech should be making the same as the starting QB at Michigan.
And before people say "But football and basketball make the money, they should be paid!" While I agree they make the most money, the schools get the money and often have to support absolutely awful sports which lose money in order to comply with Title IX. A grand total of 23 of 226 public institutions who reported their budgets actually made money off of athletics (source:
http://www.usatoday.com/story/sports/college/2013/05/07/ncaa-finances-subsidies/2142443/ ) So while programs may be making money, the athletic department as a whole could be in the red.