If Fellay's excommunication is ever lifted and he becomes a diocesan ordinary (which, absent repentance and penance, may God forbid) of the actual Roman Catholic Church, will you expect his priests to obey him? Will it depend on his intentions? Does the end justify the means?
In this case, yes. Eternal salvation is at stake here. Blind obedience to a corrupt, non-Catholic, pedophile supporter bishop is not likely to get one to Heaven.
There is such a thing as ecclesiastical abuse of power. All ordinaries are obliged to command legitimately. They may not command what would harm the faith or the Church or what would be detrimental to the salvation of souls. Many do just this. When they do, they must be disobeyed.