The third option is coexistence, though this too is something writers seem to be bearish on (Egan's Diaspora gives it a bit of consideration before simply killing off most organic life with a gamma ray burst, which I found somewhat cynical and or even spiteful, given the timing).
Only in the terrible prequels written by Frank Herbert's idiot son, who decided that a rejection of machines replacing humans = literal Terminators.
One of the more interesting things about the Butlerian Jihad is that in the end, without thinking machines, they instead turned humans into machines.