Hmm, maybe it has to do something with Kaidan rather than the council then. I couldn't shoot Udina the first time around because Kaidan wouldn't trust me and I had to talk him down, after which he shot Udina himself. No paragon/renegade options for me that time around. They eventually back down in both scenarios, I just had to go through a lot more conversation before Kaidan would trust me. Did you have a previous relationship with Kaidan in either playthrough? I noticed that the playthrough where we had a previous romance was also the one where he immediately trusted me.
Just imagine if Bioware publicly said "Oh hey everyone, you know all those decisions you've been making for the past three games? The Reapers were controlling you the whole time." That would go over so well right? People are just trying to rationalize everything because they don't want the endings to seem as bad as they really are.