I can understand the reasoning - Padme is the axis that Anakin’s downfall balances on, so finding a Padme-centric way to pull apart his friendship with Obi-Wan sounds like a slam dunk in terms of consistent and efficient storytelling. But in practice, I agree it was right to cut it; Anakin’s falling out with Obi-Wan is already set up thoroughly elsewhere, and adding a mistaken affair would have been confusing in a film that’s already stuffed to bursting.
I know Hal added those scenes back in with LoE, but I don’t remember where off the top of my head. I’d just count the number of scenes they could take place between, divide them by the number of cut scenes, then pop them in at equal intervals. That would at least give you a starting point to begin evaluating their placement.