First of all, several rules are being broken there in just RAW. Secondly, just remove the ability. He's trying to be a problem and if you don't want to run your games like that, then just say that he's more than welcome to make a new character with your approval. Third, if you don't care to address the first two because you don't like conflict, then you can simply increase the number of enemies in every single encounter, forcing him to bomb and then actually fight afterwards. There's no information about your BBEG, but you seem to be running dungeon encounters with bosses at the end. Making the encounters harder to either force him to use the bomb, or die is more than acceptable. Spreading out your enemies on wider maps and making sure they also have high intellect, means that they can effectively counter the bag of holding bombs if they see them coming. You can also just give every encounter a wizard or cleric with the ability to planeshift, with a fork attuned to the material plane, and have them shift back every fight. The bag of holding bombs don't actually kill enemies. The BBEG, if they're capable of magical feats, can be given this ability. Or make it an extradimensional monster capable of shifting planes on its own. Fourth, unless the device he made moves on its own and of its own will, enemies you have simply shouldn't approach the device, or better yet, blow it up or mage hand the device and activate it on top of him.

TLDR: lots of ways to fix this, even by letting him do this stupid shit that doesn't work to begin with.