Never forget two names: Aaron Hernandez and Zach Smith. Chris Doyle's past issues pale in comparison, but his hiring follows the same trend. That is, if Meyer thinks you can help him win, then he will overlook any and all character flaws.
Would ND have won a championship with Meyer as it's head coach? Possibly (he certainly would have had more wins than Weis in 5 years, but doubt he would have stayed at ND longer than Weis did and ND's rebuild probably needed 4-5 years given the state of the program in 2004).
Would ND's reputation have been permanently damaged in the process? Definitely.