Everything on the ship at the end was a mess. There's little that could be done to fix it, other than to completely rewrite the whole thing.
Or perhaps we see David die, then when all is over and everyone is asleep on the covenant, Walter bursts an original alien. With no David, and no control, it would either run amuck on-board or wait for the arrival on origae 6, and all the characters (including Daniel's) sail off unknowingly towards a horror show and certain death. Ferrying the devil into Eden.