There could have been many ways. When you show up, maybe some of the older Prometheans that have been hanging out could have immediately joined your assistance in killing the Covenant. Didact awakens, maybe takes some over but not others. You realize that those things still have a shred of humanity. Maybe show them doing something compassionate in some form or another trying to help humans who go down when Infinity gets attacked (instead of just fighting and fighting). Then show the Didact turning other humans into Prometheans, creating a full understanding of just what's going on. Obviously the immediately transformed would be under full Didact control. Then the question becomes how long does it take for them to regain that understanding of their humanity and their ability to resist?

343 could have done so much. I just came up with all of this right now on a dime. I doubt they were very interested in fleshing it out or making it work. Or as Quirel said, that objectivity.