I'm wondering if you are sitting too far back. I have a bunch of Brooks saddles and don't sit far enough back on any of them to be in contact with the rivets. So, have you tried moving the saddle back a little on the post in order to move forward on the saddle a bit?

Otherwise, I don't believe you should mess with the rivets. You might damage the surrounding leather also. It is possible, I suppose to have them all removed and replaced with flatter ones. Or just sell that saddle to somebody else and buy a model with the copper, flatter rivets.

But I really think it is a fit issue. You shouldn't be sitting on the frame, which is what you are doing if you can feel the rivets. Just my $.02.