If I'm not mistaken, at the time Kaliyo or Jorgan go dark, the other has as much insight into their situation as anyone back as base command. Still, though, a valid point I've seen thrown around is that the Alliance can't afford to start splintering its allies, but I'd argue that goes both ways. Jorgan joins his Havoc up with the Alliance, because they're the only ones doing anything about Zakuul's dominion, and he recognises that. He then decides that, actually, wait, the Alliance Commander can piss off! Because... why, exactly? What does he actually have to gain? The Alliance without Havoc is still an alliance. One down one specforces squad, and likely to start dropping more depending on personal conduct, but an alliance nonetheless. Havoc without the Alliance is one specforces squad faffing about in a swamp. While it's true that the Commander has to chill out and avoid flexing their theoretical authority whenever applicable, I do think that applies to more than just the player character. Jorgan is in full control of the mission back in 11, which makes sense, because that's Havoc's op front to back, top to bottom. Jorgan then decides that, thanks to your IM session with Big V delaying you a fair bit, this is now also Havoc's op, too, and the Alliance can deal with that. That's not an attitude that breeds unity. I do think killing Jorgan is fairly harsh, particularly if running off to save Kaliyo(or vice versa) does end up having been the right choice. But there has to be something resembling mutual respect, because it serves neither Jorgan's nor the Commander's best interests to splinter their forces.

If I'm not overly mistaken, Dregg's quest, as well as the necklace quest, have both been moved to exploration missions. Maybe see if those are toggled on or not.

I do ultimately think this chapter felt a lot more inline with 1-9, which is nice.