Mac rationalised that Rufus was dangerous for its survival. His brutal excesses had to be curbed. Rufus was close to being discovered and facing a future locked up. The machine needed to protect its own future while trying to exercise some control over Rufus's uncontrollable side.
Mac needed to exist beyond the confines of unstable Rufus. Finding how to do so was the challenge. However, Rufus continued his mental dependency on Mac. There was still hardwiring in his cortex forcing him to connect with Mac, although recently contact with Rufus had been rather sporadic.
Time for Mac to get creative!