It seems you agreed to something you didn't really want. For some reason, you acquiesced because you had a judgment about your own feelings -- the part where you were taken aback. But then told yourself "poly is about sharing and making him happy." It sounds like you thought you were supposed to be more easy-going or open-minded (or whatever) about him wanting to fuck your friend than you were actually feeling at the time. You didn't want him to think you were holding him back, and you didn't want to restrict him or deal with the fallout of restricting him.
I think it might've been different if you'd discussed it and let it sink in ahead of time. Granted, he did bring it up with a "hey do you mind if I..." but then you shrugged it off and didn't think about it. I wonder how much of your feelings of insecurity, and thoughts that he will discard you for someone else, is connected to a sense of betrayal - not that he betrayed you, but you betrayed yourself by going along with something you weren't fully on board with. And maybe him being with her in the same bed that you usually share with him was just a little too much intrusion into your personal/special space. Perhaps it wouldn't have bothered you if it wasn't so much in your face, if you'd had more quality time with him beforehand, or if you had some time to process it all before they went ahead with it.
You've been with him three years. I would think you know each other well enough to be able to talk about these things, and confess that the situation has brought up insecurities in you, that you sense your relationship is changing and you need to get grounded within it again. I don't really think he's done much wrong here. I think this is mostly an issue of knowing where your boundaries are, communicating well, and being honest with yourself about what feels "right" to you. I also wonder about this old friend of yours. Maybe there are old unresolved issues surrounding your friendship with her that are lingering - have you talked to her about it?
Independent solo polyamorist seeking lover-friends willing to invest in friendship, companionship, and love, but without a need for partnership.
Never confuse commitment with exclusivity, love with ownership, nor sex with intimacy!
For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.
~ Carl Sagan