Honestly if it were me, I would move on and look elsewhere. You've mentioned several structural changes during your time there, and these changes have caused cultural changes, too. IMO, the culture has shifted to a point where you cannot agree with it. I find it absurd to have to report to someone you aren't supposed to report to...but then get punished for not reporting?? Your manager is also spineless if you ask me. Ugh, don't get me started on a similar situation I dealt with. With your experience, you should be able to find a new job with a culture you are in agreement with.