I just had one of my girls spayed and she did fine with a cone. Although she had disolving sutures not staples. Possibly the staples are causing the problem, I would think they would be quite irritating. Also is the cone the right size? Sounds like it could be on the short side. Perhaps a mild tranquilizer would help. What does your vet say?
She's actually doing much better. We ended up dressing her in 0-3 month Onsies, they worked like a charm and they are soooo cute! Yesterday was Dora's first day without a cone or a Onsie while she was in her crate. All went well! She and her roommate Toby (the first mini-doxie we adopted)were able to hang out in the garage together today when I went back to work after lunch. It's great! We missed our little jumping bean.