For anyone who stumbles across this question.
I am actually looking at this same issue myself, per my boss wants GUI access for our database for himself and the developers at my company. I have found that Jetbrain's Datagrip works for 2FA (key and Google Auth, in my case), albeit it was initially a little bit finicky to actually get the auth codes through and connected.
I do not know what pricing options Jetbrain has for Datagrip since I have access already through our PHPStorm subscription. As well, I myself haven't really used the tool beyond connecting to the DB and describing tables, so I do not know how robust it is and if this particular GUI will actually fit my dev teams needs.
As an aside, the only other viable solution I have found for having 2FA compliance would be moving my Google auth off of the server and into a remote VPN solution.