Harbaugh's overall record post Kubiak is 64-49, which includes going 2-4 after Flacco went down with the ACL and then 3-7 in games that Lamar hasn't started. If you want to include the games Lamar started but didn't finish, that makes that 3-7, 4-8. So Harbaugh has gone 5-11 without a starting quarterback.
I understand being frustrated with Harbaugh but to use the argument that he doesn't win when he doesn't have his starting QB playing is a poor one. Outside of Kyle Shanahan's voodoo in San Francisco, I would make an assumption that pretty much every head coach struggles without a starting caliber QB in the lineup (albeit, I'd like to do a deep dive to confirm). That's probably the reason why so many franchises turn over their coaching staffs every few years because they have crappy QB play.
Bottom line, any coach you bring in is going to have a tough time if the QB position is unstable.
I think they've underachieved WITH QBs like Flacco and Jackson personally. I pin the mediocrity of the team with Flacco, post Kubiak, on John's decisions to bring in Trestman and Mornhinweg and the style of offense they ran. That's John's ultimate responsibility.
Not advocating a coaching change every year or two. Far from it. John's been here 14 years now, it's okay to go a different route. The game day failings I see in Harbaugh are consistent and have spanned a LONG time.