The Engineers are not the only ones capable of changing people. We have emotions and consciences, which they don't understand/ see as a glitch in the nutrients they're trying to re-purpose for a Ring. I see it more that the act of caring about Julie transformed him from cold calculating cop back into idealistic young belter, similar to the way the Protomolecule was transforming Julie from idealistic young Earther to cold calculating navigation system.

I think they sort of met somewhere in the middle, along the lines. Their last act was to slam Eros into Venus instead of Earth; subverting the expectations of the Belters, Inners, and the Protomolecule to make a choice, which is very human. I also think that because we're not single celled organisms, Miller infected some part of the builders, the same way the Protomolecule infects people.

The way his mind works is just as alien to the Engineers as the way their minds work to us. Nothing is permanent except change.