I think the Big 12 found they have little authority to act on Baylor; that they have no specific rules on this type of situation; and remember even Penn State wasn't getting kicked out of the Big 10. I think the Big 12 could make a strong case that Baylor has not lived up to the Big 12's standards, which each school has agreed to, but the lack of specifics would make it difficult to enforce. Though, in Baylor's case, the Big 12 does have the advantage of being able to show a "pattern", with Baylor having lax enforcement and little institutional control, when combined with the drug/murder scandal in the basketball program a decade ago when Dave Bliss was the coach.
The really odd thing, to me, is that Baylor represents Texas Baptist churches -- I would think that organization would be making demands and even threatening to shut down sports or even close the school after the two scandals this century. I'm sure we'd have seen BYU sports shut down if we had just one equivalent scandal.