Would he really balk at using the protomolecule to further his agenda?

What matters is that they're using the protomolecule to remake human bodies, and they aren't able to control it with perfect fidelity.

If Strickland or Merrian or whoever is using the protomolecule to reengineer a human body, they're taking one complex system and overlaying another one.

"I mean about using the protomolecule sample to try and get in touch with Detective Miller."

"Are you asking me if I'm using the protomolecule to drive the inner planets troops off Ganymede, and strengthen my control of the outer planets?"