Obviously none of the major economies in the world trades on WTO terms if they can agree a better deal. WTO rules are a minimum standard for international trade, that we've all signed up to. But if a trading block wants to be awkward it is a perfectly reasonable basis on which to trade with them; alternatively take one's trade elsewhere. It's a big world out there; nothing ventured, nothing gained.
The only reason all member countries have to rubber stamp something like this is not for reasons of democracy, which the EU has proven it does not value, it is to avoid, as much as is possible, having to change. Tie such things up with the ministers and the Commission is then free to get on with whatever it wants to progress.
IMO the horror expressed at trading under WTO rules is simply part of "Project Fear", as it seems to have come to be known.