Yes, absolutely also one of many favourite scenes from the series so far. This unfortunate revelation has my mind churning for all the implications it has for Jun/ko as a character (so, so many), as well as for the MC and the role they played during that turbulent time in Jun/ko’s life.
I agree the father is likely dead, as I can’t imagine Gensai allowing that sort of “loose string”. I’m not sure about Jun/ko’s involvement in it, though. I can see it playing out as you say, with Gensai seeing that situation as an opportunity to get rid of a rival and gain a potential weapon - Jun/ko - at the same time.
I’m not, however, sure about Jun/ko actually being the one to kill him. (Maybe Gensai somehow managed it and that’s how he first gained their trust?).
I say this only because I feel like that would require Jun/ko to see what their father did as wrong and abhorrent, which it absolutely is, yet when they’re confronted with the idea that the MC has left them and is now, in Jun/ko’s words, infatuated with this child for their “purity” - the condemnation seems to be only in the fact they’ve been replaced, not necessarily the fact that Masami is a child. (if that makes any sense).
My point here being that I think Jun/ko’s extremely distorted view of what (healthy) love is - the father who abused them, the Gensai father-figure who physically punished them and was emotionally distant, the lover who indulged their darker impulses and killed the person who became her non-sexually-abusive father-figure (whom, for or better or worse, Jun/ko genuinely loved) right before abandoning them- may have kept them from turning on their father of their own accord.
I could of course be completely wrong. Just because Jun/ko seems to accept/excuse the abuse they received from Gensai, and even the MC, on account that that’s the sort of love they were conditioned to understand, doesn’t mean they wouldn’t still have hated their father to the point of killing them, or even just done so to receive Gensai’s gratitude/training.
(minor note- I took “peerless samurai” to mean they were without equal, as in, extremely talented, though your interpretation also makes sense)
Sorry for babbling, I’m just fascinated by how this whole ordeal leads us to re-examine an already interesting character and further complexifies(?- that’s not a word) the dynamics between various other characters. I’m also in no way an expert on the psychology of these sorts of issues, so I apologise if anything I’ve said is wrong, offensive or just outright stupid.