Have "738 impermissible text messages and 528 phone calls" - No big deal
Threaten to deport a player - No big deal
Have a man play on the women's team - No big deal
Lie to the NCAA on a non violation - End his collegiate career.
Going off your point...if the NCAA went to Baylor and asked them about these calls and texts and they lied then they'd be in a lot more trouble. They basically said, 'Sorry our bad, we'll go on 3 years probation. Is that ok?'
Lesson number however many times people have gotten in trouble over the history of the NCAA: Don't lie to them. They don't like it.