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I think the creators have a bad (or good depending on your perspective) habit of deliberately leaving plot threads open and hints scattered about the place so that they could theoretically pick up on them later down the line if they wanted to.
Kirby is a good example of this.
Throughout the series we get weird little lines and glimpses that sort of make sense, but seem oddly out of place; a good example being the way his phone has his own daughters name listed as 'April O Neil' rather than say 'April', and the oddly specific point made that he is a psychologist rather than a normal scientist. Thinking about that for a moment - why bother making that specification as a writer? You could argue its just so that he isn't the go to answer for that episode, but then why deliver that in such a weirdly pointed way? Its as though the writer 'wants' you to know this specific point.
I think whats happened over time is that Kirby has had the groundwork laid for a potential reveal later down the line that he is - in some way - a traitor.
Personally I suspect this will come about as a means of triggering the final stages of the Dark April plot line; in that April will discover that her dad was actively collaborating with the Kraang to create her, that her real mother never existed, and that he was assigned as a specialist in psychology to monitor her development until she was ready for the Kraang to use.
I also suspect it will be revealed that he eventually did get paternal feelings for her and ran off to NYC in an attempt to hide himself and her from them. While in captivity he survives because he agrees to help the Kraang find her again - and the brain control device was simply a means to ensure the loyalty of an unreliable human 'ally'.
Later on, he becomes more protective of her partly because she is still his 'bargaining chip' in case of the return of the Kraang - so the idea of her becoming more independent and more reliant on friends and/or potential boyfriends means a loss of control and influence he has over her.
Anyway I think eventually this will all come to light as April discovers the truth, Kirby tries to explain that, that was the case at first, but that he has since truly seen her as a daughter.
April however isn't listening and goes off the handle (largely due to the crystals influence). If she were to destroy Kirby (say similar to how Phoenix kills Cyclops in X3), then it cements her as a villain - while still giving some audience understanding for her action.
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