I'm currently listening to the BBC podcasts on the affair and one of the independent investigators said the same thing.
You have a level of fraud/theft which presumably is low, then introduce a new system which sees suspected theft/fraud reach a significantly higher level. You'd think someone might make the connection.
The podcast says that when the suspicion that Horizon WAS the problem finally dawned on the Post Office, instead of holding their hands up, they actually doubled down and started dragging their heels, witholding documents and generally reducing cooperation. Anyone who knowingly took part in that should be going to jail.
They've also effectively stolen money off those sub-postmasters who they forced to repay non-existent shortfalls. They're no better than scammers, who would certainly go to prison if caught and convicted.