Well they weren't rampant, they didn't exterminate organic life. But yes you do have to take it on faith that rampant AI is something to be feared.
Yeah, faith indeed... Because rampant ai cannot have wiped out all organic life in around a billion years or so in the ME universe, since there existed organic leviathans to invent catalyst's and reapers. So the only evidence for it's possibility is mention of small scale relatively limited conflict. I don't do well at all with faith.
But all of this is old ooooold ground...
The point of it is... Make a better ending next time, so we're discussing something worthwhile and subjective, such as morals, rather than details and oversights of the writers. And in my oppinion... make it even better and emotionally engaging the next time. A good bittersweet ending is not the absense of both bitter and sweet, but both combined.