As far as taking the Ferengi out of the game, personally, I'd say just don't use them. You don't have to change canon and remove them entirely, just don't bother to include them in your adventures.
The only things I don't use for my Star Trek campaign are the events of Star Trek V, as Gene considered them apocryphal. Aside from that, I try to reconcile everything as they happened in the series and movies.
Of course, I don't go into the Delta Quadrant, so I usually ignore most of what happened on Voyager, but that's only because the PCs aren't there, and I won't ever send them there.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz