The first item to remember with this is that these are NOT modern religions or religious groups. These folks, particularly the Haelynites among them, really believe that this world is secondary to the hereafter - that, yes, it IS better to die than to break faith with your god, and that a true believer must CERTAINLY die before leading others into sin and blasphemy. The more forgiving ones may understand that to fail to do so is a sign of weakness, not of outright EVIL, but it's still a failure on Geraldine's part to them.
Second, sure, politics are involved. With Diem in there, that'd be hard to avoid, but nothing in Anuire is decided without politics. That said, even the folks who aren't threatened by ILIEN are threatened by the OTG church. They have to step on it HARD to try to keep it from spreading, which means they need to publicly smack down anyone who's involved themselves with it to make a point. And, Linde, you may have been the first to publically declare them heretic, but the other regents didn't have them in their provinces. I can't speak for what's been happening from a first-person view, but from the outside the Countess's actions look very self-serving - she didn't act against the OTG until 1) she was safe to do so, proving (at least to a strong-believer priest) that she cared more for her own skin than her faith, and 2) that she was more concerned with bringing the temples in to try to ward off Diem when it became clear she couldn't do so herself than in doing The Right Thing.
Third, this Tribunal is clearly set up for multiple conflicting purposes. On the one hand, the selection of members must've been meant to satisfy a lot of irate people - why else would Archduke Diem and a Boer noble paladin from a thousand miles away be included on a panel judging questions of religious corruption?? On the other hand, the Pontiff has systematically pissed off as many members of that panel as possible, starting with ignoring, from what I hear, the judgement of the CoT, and proceeding to deny the panel's members any significant time to question Geraldine or witnesses, investigate evidence, or generally do much of anything except accept the judgements of unnamed IHH priests that he hands them. Given evidence that they probably don't feel they can trust and an (apparently) partisan Chairman who keeps pissing them off, it's not surprising that they'd err on the side of making sure a possibly-blasphemous Countess isn't left on the throne of one of the most powerful provinces in Anuire, is it? From their perspective, they lose nothing by convicting her falsely (and she'll surely be comforted and rewarded in the afterlife if she's innocent), but if they falsely clear her of charges, then they could have a disaster on their hands down the line.
All in all, while the Pontiff may have saved Ilien's bacon for the moment, I think the Countess would have been better served with a more 'proper' Tribunal - one given time to examine matters, to speak with her, to really judge her actions instead of simply Passing Judgement. Denying this group what they consider their proper respect and the time to make informed decisions only sets them up to grumpily vote for a bonfire then stalk away furiously. Sure, Diem would still vote for burning regardless, and the OIT is known for taking a damned hard line against things like this, but the RCS, given time to consider, is not an unfair group, the WIT would have listened to the evidence of their own eyes and ears much better than to Wallac's dog-and-pony-show, and neither Mordred nor the ETN seem inclined to burn Geraldine for the sake of safety even now.
I think, regardless, she'd have been forced to step down as regent, but I think she'd survive. Which I'm sure would be very preferable to her than the alternative.