I think "masochist" button is the biggest button obscuring all the others. 
Note that I originally planned this as being one of two "I Win" buttons, but then I realized that you guys might invent the 'masochist' buttons instead.
I think it's axiomatic: players will create situations more dire than the GM had planned.
"GMs will mistake character motivations for character motivations until it is too late." That one was what got us last time. The best example I saw was in a Vampire game where the player wanted to explore the strange new power and the character was afraid of it. So the GM kept offering opportunities where the forbidden power was a viable option, but other ones were better.
I'd actually like to see some retconning, though my request goes beyond that to ask that we also hear some of what Sophronia's actions might/should have been from the SG's vision of the character. I've generally tried to operate on what I perceive character motivations and archetypes to be and I've had trouble figuring out Sophronia in general. It seems that was probably because of what JL had posted - the pre-existing character and player's concept were in conflict on several levels. It'd be nice to have a decent idea of who this person is that we've been in the same covenant and worked together with on several occasions for our own role-playing purposes. In particular for a lady-lovin' magus. cough
Retconning may not be necessary. It could be that Sophronia's vanity and ambition exceeded her capabilities, and she gets recalled to Coeris for re-education. It is reasonable and possible for people to hang all the baggage of GF on her, and she exits the Tribunal. Her actions still stand, but the effects of them are mitigated to some extent.
I blame Adorjan. Bad enough that he invented a Cruciatus Curse in life...then he went and invented the Imperio and has been using it on poor Sophronia all this time.
Sophia the NPC was reserved and calculating, the sort where you never know what's going on in her head. She would be friendly and amicable while still imparting a sense of emotional distance.
Sophia the NPC would not have found it unreasonable for like-minded people to congregate, but if she did, she would not have made a scene. She's not a risk-taker-- she takes bold action only when she's certain of the results.
Again, my dear girl, who is this Adorjan you speak of? As I said, no such magus exists or existed.
Honestly, I had this same interpretation about her, but I never received any reinforcement. Did she move from Libellus or repeatedly request transfer because she knew something, had an ace in the hole, or was she just ordered off there? I couldn't make sense of the reason why she'd leave Libellus. If she's calculating and takes action only when certain of the results, she had to have a very good reason (it could've been wrong) for taking action. I didn't feel I had anything to back up her actions as a player, so I was all over the place, quite literally flailing about.
And let me say that this is not a knock against Arya, more so myself, for not doing enough due diligence to take over the back story. If you thought her actions were all over the place, well, they were, and so did I. That is one of the chief failures of the character. I also didn't let her ruminate enough. The concept I'm working on now I've been thinking about for a few weeks, primarily for another saga. He's...interesting.
Unless anyone stops me and says, "No! Wait! I love politics!" I'm going to try to blow through Tribunal as quickly as possible.
"Politics? I just want to get back to my lab. My master told me I should come here, and there was this dinner party I wanted to attend, but apparently I'm not cultured enough or some silly thing."
Kinda stuck with Hiems and Cygna.
I can't see any of them reacting differently.
Thing is, that leads to Hiems exiting the saga, either more-or-less happily, or by suicide and tragedy 
Hiems can leave the covenant and still stay in the saga, by wrapping two different stories together. The Earl was going to throw some lackey into the covenant's convenient manor home, to fill the void left by Montalt's disappearance. He can send Lisette instead 
Also we can go one of two ways for Lost Love. Either she can have an arranged marriage to a new lord, or she can marry Hiems and cheat on him. Up to you!
Cygna would never cheat on Hiems. Just sayin'.
(of course, she has checks calendar 45 more months before she can admit, even to herself, that she feels anything, but still)
Yeah, but cygna is the most perfect woman Hiems has ever met. He wouldn't be surprised if she was cannonized one day 
Mouais... Not quite satisfactory to me. Thing is, so long as she's around, Hiems has no motivation to do much, and won't come close to the covenant. He's just happy being with her 
That's better, although not well.
She can openly cheat on Hiems, he will accept it, even if he doesn't like it. To him, not only is she her own mistress, but, after his loss, he's too afraid to lose her again.
A new marriage would be better, although if they could still see, knowing she's love him, that'd still be something Anyway, I can't see him appearing before cygna again should something like this occur. He'd probably seek out any covenant anywhere.
See my problem?
There is no problem, move along.
Lost love is that, it's lost. It's a personality thing. Heims can't get back what was lost. If he's with her now, she should mourn the time that they were apart and be unable to move forward because of that, which creates all kinds of new and interesting possibilities.
Even if Sa Dame is living at the covenant?
Flint was destroyed. The Welsh hold de Montalt's traditional home, Mold Castle. The Earl needs a baron, or someone to fill the role of a baron, and there's conveniently a nice manor house right there in the middle of Neston (Gallus Florensis). The "Great Hall" was built by Justinius, sure, but everything in England is the property of the King, so the Earl is well within his rights to say, "This is the new lord and lady of Flint, and they're moving into that manor you've got there."
Not really... if he's as devoted to Lisette as you say, then when she is sent to live at Gallus Florensis and act as Baroness of Flint, why would he not follow her? Cygna's sanctum is off in the woods anyway. Lisette can convince him that the two of them "will hardly ever see each other," and in any case, she probably wouldn't care if he thinks it'd upset Cygna. She'd make the appropriate sympathetic noises, and then do as she's been commanded anyway.