Man, I don't think I agree with anybody!
Don isn't good at business. This is a repeated theme in the show. Season 3 revolves around him getting a company-defining account dropped in his lap and then blowing it because he can't handle accounts, but there are plenty of other examples of Don losing accounts basically every time he opens his mouth. It's not his job to be good at business. There are other people in the agency for that, and they're generally quite good at their job. You should be able to tell just from the last few episodes that Pete and Roger, at least, are good at their work.
This episode is about trust, and what you know that others don't. Pete and Cooper and Joan knew about the IPO, and if they'd told Don, he might have acted differently -- but they didn't trust his reaction enough to tell him. At the same time, Don is the only one who was actually at the dinner, so he's the only one who saw that Herb is deliberately trying to destroy the account. Herb's previous ploys had the effect of getting Herb stuff he wants; this one can only piss off Don and damage Jaguar's campaign. But Don's record of pissing off clients is so bad that nobody trusts him when he tries to explain that. It's also worth noting that if Don had let him get the local advertising he wanted, he wouldn't be trying to kill the campaign, so he still doesn't get a pass from the perspective of handling accounts. Fundamentally, the conflict between partners is a result of mistrust, which will not go away as a result of this merger.
Joan is absolutely angry more about Don's pretensions to high moral principles than anything else. I didn't even think there was another reading of that scene! Remember, Don is screwing Herb because Herb screwed Joan. He thinks Joan will be happy when he goes into that conference room. But Joan isn't interested in a white knight, and she recognizes that losing Jaguar will not erase the rumors around the company of what Joan did to get Jaguar. As Joan more or less explicitly says, if she can do it, so can Don.