The only way I know of to get rid of an upgrade would be to get rid of the object, then you can place a new one.
Also I've discovered if you've completed Nerd Brain and earned the Handy trait, don't Instant Upgrade your toilets. Instant Upgrade will do the composting container too.
Oh, and the reason it's even a thing- the composting container provides the compost for your bug houses. If you have bug houses and you're feeding them regularly, the toilets won't blow up, because you're using it up. But if you don't have bug houses, you don't want that upgrade.