I don't think anything in the episode outright debunks the theory (echoing post 14 here) but I do find it so very Disney that they went out of their way to provide ammunition against the headcanon this episode. Was especially rolling my eyes at the scene in the elevator where Sylvie asks what she was even arrested for and gets told by Miss Badass Time Cop that she doesn't remember. Lmao really bitch? You expect me to believe you forgot Sylvie got arrested for the crime of being a woman? They couldn't have just written confirmation of that? It isn't really a mystery - she's right there! Yes, they used that line to make a point about how fascism doesn't care but they could still have made that same point.
I also agree that there's more to this than Sylvie being arrested simply because she was born as a female Loki. If that were true, then her nexus event would have started either immediately at birth or possibly immediately upon being adopted into the royal family. I could be wrong, but logically, there would have to be more to it than simply because Sylvie is a female version of Loki.
In fact - the twist may be that she's not actually a version of Loki at all. Or that all of the "Variants" aren't really even variants at all. Whoever or whatever is behind the TVA probably has something else behind their kidnapping of all of these so-called "Variants".
Either way, I do agree that Ravonna completely knows why she arrested Sylvie. She had been chasing Sylvie for years. She either didn't want to admit the reason or she was being smug and screwing with Sylvie.
Also, Episode 4 was WAAAAAYYYYYY better than Episode 3.