Not sure why you're basically absolving UM on this, but here's an outsider's take...
1- there's a vast amount of undeniable evidence that Michigan has been cheating for years.
2- the staffer has been fired, but only after Michigan had been publicly outed months after the investigation started privately and with Michigan's awareness.
3- the coach, who has been penalized for other NCAA/B1G infractions just this season, is to be held accountable for direct and/or indirect knowledge of everything going on within the program. There's this concept of lack of institutional control, so a leader can't just look the other way or claim ignorance of wrongdoing underneath him or her.
4- there's this thing called progressive discipline and this is not a legal case in a court of law, so there's no requirement to have 100% of the evidence presented before initial discipline is handed out.
5- Harbaugh's three game non-sideline game coaching penalty is just the first step and really is just a bit of a slap on the wrist with more measures likely.
6- do other schools have cheating going on right now and in the past? Yup, pretty sure there's something going on at many B1G schools but this is not what's being investigated now. Will Michigan report something going on elsewhere? Seems like that will happen at some point. That's within their rights as a B1G member. But it doesn't absolve Michigan from what they're being investigated for now.
7- Michigan in the court of public opinion is really looking poor on all of this. Poor Head Coach, AD, and President perceptions abound. Supposedly their BOT's, major donors, and university professors' views are mixed on it.
8- usually when something reaches this point this fast, the outcomes are not good for the leadership. Seems like that's what is going to happen here, too.
9- whether in a court of law, the court of public opinion, or in a member-driven disciplinary process if remorse is shown, the penalties are usually handed down with that taken into account. There is little of that being shown by Michigan, so they are going to have to risk their track of behavior impacting what may or may not apply to their final penalties in this regard.