Hopefully her response is positive, as your reasons make perfect sense to me. I also think the only thing you could've done differently is to not ask her not to talk to him about it - her reasons for wanting to be able to talk to him about it also make perfect sense.
I'd just apologize for putting her in a position that made her uncomfortable and say I'd do my best to not do it again, and that I hope she would speak up if she felt uncomfortable with any of my requests in the future. Yep, I would suck it up because she felt bad, I wouldn't take it personally as nobody did anything wrong, was just an unexpected emotional response. Unless there's been anything else that's happened, it was just asking her to keep it to herself that was a problem once she realized she had questions to ask him about it and didn't know if she'd agreed to never bring it up EVER since you didn't originally explain to her your "why" you didn't want her to talk to him (yet).
Maybe requests like that are suitable for a friend, but not a metamour under this circumstance. It seems like you two have a good relationship so I wouldn't shut down the lines of communication unless she can't let it go and is bothered on an ongoing basis by it.
Happiness will never come to those who fail to appreciate what they already have.