While FF6 wasn’t the first RPG to have temporary playable characters, it was the first that changed my perspective on the potential of the genre. When you meet Banon, not only is he someone the protagonists look up to, he is essential to their success.
You’ll find in battle that he’s incredibly powerful, essentially able to cast Cure 2 on your entire party every turn indefinitely. This makes one wonder why he’s so impressed Terra can use magic, though technically Banon’s power doesn’t come from magic and future versions of the game change his power from “Health” to “Pray” so it’s basically a spiritual power nobody else has and oh my god just play the damn game and don’t worry about it. Worry about Banon, because if he dies, it’s game over and you throw your controller because you last saved twenty minutes ago.
That did happen to me the first time I played it. But it was frustrating in a good way. Having to change one’s battle tactics is essential to prevent the usual monotony that comes with RPG battle grinding.
It’s also worth mentioning the cool scene where Banon rips the leaders of Narshe a new one for remaining neutral in the war between the Returners and the Empire. It’s not worth mentioning that Banon disappears around halfway through the game and nobody ever mentions his name again.
Death By Troggles 
I, too, was bugged that Banon disappears from the narrative after playing such an essential role. Yes, if this is the whole world I suppose that’s realistic enough, but if we’re following that many narratives, isn’t it reasonable for us to learn what happens to him? If he dies during the Big Event in the middle, shouldn’t we learn about it? Hell, we get to learn what happens to Cid!
I was initially irritated by the escort mission, but it definitely grew on me for all the reasons you suggested. I wouldn’t mind more of them, frankly.
Even if we don’t find out what happened to Banon, it would have been nice had someone said, “Hey, has anyone seen Banon?”
Escort missions are well-hated, and for good reason, but this one didn’t annoy me (for the reasons you brought up). It helped that he was pretty badass with the curing, and it also helped that you meet Ultros around that time.
I hate escort missions that are thinly-veiled fetching quests. But this one was different in that Banon’s role is well fleshed out, and because he’s not a helpless background character just there to push the story forward. You’re escorting him, but he’s also helping at the same time. And his role isn’t over once the quest is over.