NCAA should NOT be involved most of this for the very same reason they should not have been involved in the Sandusky scandal. They don't have the tools to deal with it, they don't have subpoena for one. Also, the NCAA rules do a very poor job related to criminal behavior.
It should have been dealt with by the Baylor campus police and Waco, TX police and campus judicial affairs. It wasn't, now the US Dept of Justice and Office of Civil Rights will be involved under Title IX violations. That is how it should be dealt with.
NCAA should get involved for possible recruiting rules violations (recruits having sex on recruiting trips, etc.) and possible impermissible benefits. NCAA rules state that student-athletes should be treated same as all other univ. students, that includes campus judicial affairs. If Baylor football players got special treatment in Baylor judicial affairs process, that is a violation.