I would disagree with that. 2/3 of the tribunal is dead, one is gone. At minimum I think this makes the ability of the temple to project its influence and power beyond Vivec next to nothing. If it wasn't for the events of Oblivion I would have said that the houses with more Imperial ties (Hlaau) would gain in power and those whose influence was not closely associated with the the Temple (Telvanni) would be largely unaffected. I think we would see the temple relegated to a position similar to what we saw the Cult take in Oblivion, an important part of the culture but not a seat of political power.
Yes, but the Tribunal had been recluses for quite some time - nobody saw them but the highest echelons of the Temple, and besides, Alma and Seht died in the Clockwork city, which nobody can get to to provide proof of their deaths. Even in-game while you're the Nerevarine the only people who believe you when you say that they're dead are Helseth and Vivec, everybody Dunmer down to the lowest commoner (including Hlaalu and Telvanni) will tell you to go and repent, meaning that the Temple is pretty damn deep-seeded into the minds of the people when they won't even believe the savior of Morrowind when he tells them the gods are dead. The Temple has been around for over 3000 years, an establishment like that
cannot die overnight.
So, we have populace that refuse to believe the gods are dead even when the Nerevarine himself tells them. We have no actual proof that the Tribunal are dead (and you can't just waive this off by saying that the Nerevarine gave the populace proof and thereby destroyed the Temple in the process, because my Nerevarine sure as crap wouldn't have done that), and we have a Temple hierarchy that could easily cover-up the disappearance. Not only that, but the Temple has just had a huge victory over Dagoth Ur, who has been their 'devil' since its establishment; there's no way the people would abandon it after such a recent demonstration of influence.
As I said, it is absurd for it to even come close to collapsing in that period of time. The only real hit they've taken is the waning of House Indoril, and despite them being a major supporter of the Temple the establishment was by no means resting upon the Indoril.
I don't think it is lack of thinking on their part, they are just leaving themselves options for when they decide to revisit the setting in another game.
It doesn't make any more options available.