i would not shoot them. i personally would just de-prime'em and then soak'em in some lite oil to make them inert and discard safely. if it was me,i would try another brand of primer (federals are my favorite)and see if your problem goes away. if the primer cups are still "high", then i would measure the depth of the flash-hole of that brand of brass. compare it to another manufacturer either in same chambering or just another large flash-hole. oh yeah,the reason i would not fire them.....if they are high enuf to be a safety issue,i would be concerned that they mite detonate while rotating the bolt to "lock" position....before the lugs get fully engaged. the drag on the cup from the boltface mite just be enuf for detonation. unlikely,but hey,why be "ole one-eye".
