If that’s the case, then we can rule out Babu using C-3PO to try to attack some of the protagonists.
Being reprogrammed certainly sounds like a plausible reason for why C-3PO would have red eyes.
Regardless, whichever side Babu’s working for is lucky to have his talents available.
While Babu Frik’s allegiance wasn’t spelled out, one would imagine that a Spice Runner of Kijimi is more likely to work with The Resistance rather than The First Order.