Can we be in communion with someone whom we truly believe to be an apostate? Someone who is conspiring to destroy the Catholic Church?
Well, no, not in the sense of obeying his heretical wishes, yet we can, and as Catholics, we are bound to pray for him, which, per Ex Quo, is what we are doing when commemorate him in the Mass. The Church (Ex Quo) makes no distinction on the state of the pope's soul, clearly she teaches that to omit the name of the pope is an act of schism. It should also be clear and if not, one must convince themself that She thought the matter out thoroughly as always, and quite emphatically does not tolerate any exceptions. The idea that "she never saw this crisis coming or she would have added the exception..." is altogether absurd.
If one has the faith, then they know Ex Quo is a true teaching of the Church, it is a teaching of the Church's magisterium, hence, it can only ever be true always and everywhere. There is no expiration date for truth and truth has no mistakes. We cannot simply decide to omit his name because of our opinion of him, the reason for this is because the Church condemns doing that.