What lesson are you going to be teaching them? "the GM likes to give us toys then take them away"? You just need to up the ante. Although if the players are too low level, anything that can kill it will kill them.
If you really want to kill it (which I think would be pretty cruel seeing how much wealth they've spent on it):
Shocking grasp (intensified, maximized, empowered) can do 78 (average) electricity damage per spellstrike. Add in the vulnerability, and you get 117 damage. A couple of those will take it out. A level 15+ magus can easily dish out 2 of those in a single round (with quickened magic) for a total of 234 damage. It wont even have the chance to use it's self-destruct mechanism.
Have you tried hitting the snooze button?
A portable hole to put what in? The goliath? The hole is nowhere near large enough for that (fully opened it has a 6 ft diameter and is 10 ft deep).
I'm also not entirely sure how they manage to get a Gargantuan creature to squeeze in everywhere. It should only be able to squeeze through areas that are at least 10 ft wide.
Now, since you say the campaign is nearing its end, I don't think there's any reason to specifically target the goliath before they reach the final BBEG. Of course, if said BBEG knows the party keeps a pet goliath around, and is ill-equipped to deal with it, the BBEG should of course do everything he/she can to either destroy it or otherwise hinder it (whether by hiring someone to attempt to do so beforehand, or by purchasing items etc that can help him/her against it during the encounter).
I will never understand GMs who seriously consider dampening their players' fun.
It sucks that you're not having any fun, something I think GMs should have too, but disallowing something your players clearly want just isn't the right way to deal with your situation.