That made sense to me. At the point he was seeing the replays of that part of his life first, it could all have been faked, as he was saying. But the infinity stones indicated it was real.

Some other things didn't make sense to me, or seemed at least really contrived, in the first episode; like, given how the TVA will reset timelines and prune variants at the drop of a hat (or the lack of a ticket), why would they even bother capturing variants in the first place? And how does it make any sense at all to ask a variant to plead 'guilty' or 'not guilty' to departing from their proper timeline when from their point of view they have no ability to distinguish between what is and isn't their proper timeline? (Yes, I get that it's illustrating a kafkaesque bureaucracy, it just seemed contrived). And would Loki really have not tried to use his magic at all until he was in the court room setting?

But those are minor quibbles really, and some of that might be addressed if we learn more about how the TVA came to be what it is anyway. The set-up of something can always be a bit clunky, and once it got past that, I thought it felt a lot smoother and really got going.

Thanos snapping his neck has its own importance given that knowing he'd wind up dead like that in his own timeline would rule out going back into that timeline as is for Loki, if that was possible. But from the point of view of that Loki, seeing Thor telling him that he wasn't so bad, and Odin saying, "I love you my sons," would also have had its own impact on how he sees himself, and how he might act going forward.

For the infinity stones, I didn't see it as a, "these are really powerful, so the TVA must be really powerful" thing, I saw it as more of a, "these are real, so all of this TVA stuff must also be real," thing. Once you accept the existence of the TVA, the infinity stones aren't the most powerful objects in the universe, they're just the most powerful objects in a universe. The TVA having them doesn't make the TVA powerful in itself, they evidently can't even use them to the point where they're junk, and we've already seen - repeatedly - that beyond having the collars, reset bombs and the... actually, I'm not sure what they're called... prune sticks? Beyond having those, the TVA isn't especially powerful when its agents are in any given timeline. I don't think Loki is so much respecting the TVA as he is just recognising the reality of it.

Although I suspect the TVA must have a nuclear option beyond what we've seen, given that we've already seen them get dangerously close to a Nexus event passing a red line, so it's hard to believe it's never happened, and there's also the question of how they created the one sacred timeline in the first place.