I'm really having a hard time understanding what the point is of Threepio having red eyes.
I'll admit, I'm not thoroughly versed on the canon outside of the films, but I don't recall red eyes being a sign of "evil" droids. Maybe I'm wrong? I dunno, you guys tell me if there was a precedent for this.
Also, we've seen other protocol droids of the exact same style as Threepio. So I don't get it being either a disguise or a sign of an evil version (that maybe isn't even Threepio) -- unless JJ has just decided that we are all too idiotic to understand without some blatant visual reference.
I just can't fathom a good narrative reason for this beyond either the director thinking this looks cool, or thinking that the audience is stupid.