Bovxer, I can see I was typing an edit to my last message while you were typing a reply. I'd like you to check it out, because it does develop an answer to your original question, to some extent. Bascially, I think that the Diedne's re-emergence, coupled with their desire to keep secrets, creates a climate of fear that is more dangerous than any "death sentence". I have quored from earlier editions a fair bit, bedcause I think that colours my views a fair bit.
The tribunal didn't decide, IMO, if Tremere were right or wrong, merely if the declaration of war was legal or illegal. The Code is a really weak reed in terms of protecting the rights of magi, because it has a clear out: you are allowed to murder your fellow magi provided you tewll them in advance that you intend to do it.
I'd also say that the core rulebook needs to cover the entire sweep of Hermetic history in a handful of paragraphs. It therefore lacks any real nuance. Nuance is important, because you can get game ideas from it. So, although the write-ups in the House books never say "Hey, ArM5? Wrong." they do say "ArM5? Very sweeping, simplified version of events." For example, in this thread you have talked about House Bonisagus as abandoning the Diedne: its clear from the House write-up that much of the Trianoman faction was on Diedne's side, and they may have worked out a sort of underground railroad. House Jerbiton claims not to know where the Evangelists (the two groups sent out to paralell the development of Valnastium) are, but there are bards in House Jerbiton who look a lot like Druidic bards. I'm not saying either of these are "Here's how they escaped!" revelations. I am saying that throughout the editions there are trapdoors in the history that let your troupe say "They are still around." (In the last edition there were a group of Bonisagus who told people flat out they were Celtic bards who joined Bonisagus instead of Diedne.)
I think that we played that out in ArM2. The current stance, which is that they m,ay or may not have desreved what happened to them, is bascially an attempt to keep all of those optiopns open in the vanilla setting. The reason I object to your read is that it assumes the Druids didn't deserve what happened to them. Now, that's a perfectly good rerad for your own game. In the core setting, though, you can't prove that when the Guernicus piled up all the evidence and burned it, to stop the diabolic rituals spreading, they weren't 100% on the level. In the setting I like the option that they -might- have been.
House Guernicus destroyed the evidence afterwards. Now, you can say this is because they had a guilty conscience, or because they were defending the Order from its corrupting influence, but they did much the same to the Tytalus, too, so their methodology is consistent with an uncontested case.
Dark Secret doesn't mean you immediately face extermination, it means you, as the player, agree to make an issue of this thing. Now the stories you are going to play are probably not a grim death march, because you and your SG will negotiate that, but if you like you can certainly play a Diedne, in your game, that doesn't need Dark Secret. There are druidish guys in Ex Misc who don't have Dark Secret, as I recall.
I can see that, but I'd point out that even a full Hermetic tribunal doesn't reach our modern standard of justice. If you take as an axiom that genocidal war is, in setting, always wrong, then you can't get from there to the Tremere ever being right. In 1220 in game there are pagan guys in the Rhineland pulling the hearts out of people right under the noses of the Tremere. The way the Tremere are likely to deal with them, which is to genocidally destroy their tradition and explain to the Tribunal afterwards, isn't how we do things now.
It would be an interesting setting to play, though (the one-house covenant, I mean -- not St.Paul, though that might be interesting too).