I mean the issue from my perspective is just that they were kind of fucked when they decided to go down there. From my understanding (and I mean it lovingly and respectfully) they got really bad PC-itis and Sean ran away with the story and they flat invaded and entire kingdom that Sean already established had "armies of thousands". Even if you try to scale it down as much as you can to give them a prayer of a chance the issue is still that they're doing something that probably should not happen.
And the bigger issue there is you can't just flat tell your players that they can't try to do something because that's really fun-killing, but if you throw them straight into a wall that's not enjoyable for anyone either.
If they rested they were going to be surrounded probably (even if they hid the previous rooms would refill and the place would go on high alert because there are invaders) and they're dead.
If they didn't rest they'd run out of steam and eventually they're dead.
If you scale it down enough that they can actually can take out a base and a gnome king (Even if you justify it narratively by saying the mara corruption slowly killed off most of the gnomes and this is all that's left or any other plot excuse that still let's them take on the king without it derailing the entire plot to make him a MASSIVE figure in the story) your party get's REALLY bad PC-itis and starts doing really dumb shit and gets themselves killed or ruins their own campaign.
It's kind of a rough issue and all you can really do is hope that the players learn from it and use that experience to make different decisions and grow (rather than assuming they had bad rolls and just try again), OR make sure to be really careful when designing places so that the scale lets them go through it comfortable but then you make it equally not super important to the story.
I don't have any criticism of it, just from my perspective and how I interpreted what was happening it's just not a good situation to be in. (To criticize lightly if Sean weren't new to DnD and didn't make the campaign while he was a guest about HIS story it wouldn't have happened in the first place, but even there part of being a PC is to world build and add and help things grow.)