It's not a given that Title IX will even apply once they are paying the players. Up to now, the NCAA and its member institutions have denied that the athletes are employees in order to avoid the various legal aspects of that designation. Once they are paying them directly, though, that pretense is going to be very hard to maintain.
If they are legally employees, then the schools could also drop the pretense that varsity athletics is entirely an educational enterprise, and could admit that it is commercial. If it is commercial, then they might not be covered by Title IX, which only applies to educational programs. This will surely be litigated.
Of course, it's also possible that, if athletics is deemed a commercial enterprise, that donations to the athletic department would not be tax deductible. This, too, would surely be litigated.
In short, we are headed over a precipice, and no one knows what lies at the bottom of this ravine.