The Bama DL coach that resigned, Bo Davis, was being investigated by the NCAA for impermissible contact with recruits.
I have not seen any reports anywhere that claim that he "just resigned after he was found to have been illegally paying players". Can you please provide a link to the article claiming he was paying players?
According to this article:
http://www.al.com/sports/index.ssf/2016/05/new_details_regarding_potentia.html
"The NCAA contacted Alabama's compliance office regarding the situation, and Davis was questioned and caught being dishonest before eventually resigning, according to the source."
It sounds like another school heard about the impermissible contact and called the NCAA. It also sounds like Bama cooperated and removed the coach. There is precedence for that being the end of the case. Basically the same thing happened with Phillips at Florida.
I also can not find any information about Bo Davis committing previous NCAA infractions. College players are allowed to speak to agents as long as they do not sign with them or accept benefits. Many schools have approved lists of agents and direct student athletes towards those individuals. "Hooking a player up with an agent" would not be an NCAA infraction.