In case of Waukeen's Rest, it could have been handled quite easily.
Nah, you just created one potential scenario.

Thats all.
Trigger the event by seeing smoke rising from some point (perhaps even have companion point it out), then if you decide to rest rather than investigate and do the stuff related to the fire, you'd get a cutscene where the fire is largely under control, Florick is standing outside (having been rescued by the Flaming Fist mercenaries) and tells you of the situation with the Grand Duke.
What if you dont rest?
What if you go and deal with Gnolls on the road, and Zhentarim people in that cave, and Paladins at Tollhouse ... and then you return to that burning inn within single Long Rest >> aka. whithin single day?
If you manage it in a single day, a.k.a.. no long rest in between, the scenario would play out as if you had gone there directly. After all BG3 unfortunately has no way of measuring time besides days.
The situation with the Zhent caravan survivors and the gnolls would be even easier. Ignore them for too long and have the gnolls slaughter them.
Well there is allways speak with dead ... but thats not the problem.
What exactly is "too long" and when it start count?
THOSE are real problems in such scenario.

Again... "too long" would be after a long rest. And it would start by either noticing the gnolls attacking the cave or by getting the journal entry about finding the survivors.
Having a chance for failure or to miss out on some things is a good thing in a RPG.
Well ... in general, yes ... but it allways depends on execution.
I use my favourite example: Arabella, the Thief(ling).
In general ... having a chance for failure i a good thing ... most certainly 100% agree.
But the execution in game, where you either win an arugment, that is presented by SINGLE diceroll, wich sucess rate depend on ONE of your stats, no matter how important or even fitting it is for your character otherwise ... OR your character is forced to stand there with hands on his/hers hips and without moving a single muscle watch child being bitten by snake and die ... thats poor execution and therefore it was not good thing. :-/
Simmiar it would be here ...
IF the game would put us to situation where it would be clearly stated that we have to choose wich one will we help ... but i mean REALLY clearly ... it would have potential to end well, even tho it would certainly not be guaranteed.

The situation with Arabella and Kagha makes for a bad comparison though, since "failure" there is determined by a random die roll rather than by the player's choice (unless of course, the players chooses the option to "wait and see how things play out" during the dialogue).
As we are now, many (and i certainly admit that i dont know how many, but to name one ... Icelyn, this is not snarky coment btw, she said it herself some time ago) people would be frustrated.
You also should count with that there will be people who will purposefully try to break the system ... and split their group in order to help both ... or will go do something entirely different, just to see if the game will have balls to let everyone die.

You can't please everyone. Someone is always going to be disappointed by whichever method they use. As for people who'll try to break the system on purpose, let them. They paid the same money I did for the game, if their idea of fun is to see whether they can break the system more power to them.
//Edit:
I guess you haven't played Fallout 1 or if you have, didn't enjoy it? It has a 60 days timer for the first half of the main quest (the water purification chip). This is clearly communicated to the player and it adds a lot to the game. You are on an urgent mission after all and shouldn't tarry as lives depend on you.
The possibility of failure is part of the fun.
Unless your time expired just few "steppes" (not litteraly) from completing the quest ... in that case, it just sucks.

This literally happened on my first playthrough of Fallout 1... the time was up (since I went exploring a little too much) and I was 2 map squares away from the Vault. Was it frustrating at that moment? Sure. But I reloaded an older save and finished that part in time.