Prove it? No. Suggest it, perhaps.
I’ve mentioned before that Lucrezia’s own character is really the crux of the situation. The implications of the reconciliation at Nepi and her closeness with Cesare afterwards (I agree, they seem if anything more devoted from that point on, and their most extravagant and arguably selfless displays of affection come from that period) depend on what she was like. And Lucrezia is an enigma.
It’s like a scale: the more we weight the idea of Lucrezia as a blameless, innocent model of virtue and proper feeling, the less sense we can make out of her swerving around to renewed intimacy with Cesare and loyalty to family interests, except by supposing some other reason. The more we regard her as cold, ambitious and entrenched in Borgia interests, the easier it is to accept the totality of the reconciliation—and the less we need to look around for other reasons.
So, traditionally, there are two images of Lucrezia: the ruthless evil villainness Lucrezia and the sweet vapid victim Lucrezia. At the first extreme, it’s perfectly easy to understand her shrugging off her husband’s murder, but… not much else; at the latter, much of her day-to-day conduct makes more sense, but we have to assume she knew some terrible secret about Alfonso or something and was terrorized and dominated by Cesare to the point of pursuing his interests when he was imprisoned in a different country for years. The reality, I think we all have to agree, was somewhere in between; unless Lucrezia was incredibly unfeeling, it seems likely that Cesare’s hatred of Alfonso (on record) had some basis that satisfied her, but from what we know of Alfonso, not a serious plot. I don’t think he was an innocent lamb, but lbr nobody was.
(Personally, I think Alfonso very probably got up to his neck in the Colonna plots, and may have followed his sister’s lead in her open antagonism with Cesare, but without anything like her skill or nerve. Not reasons that would have satisfied someone who was not Lucrezia Borgia, but there you go.)