They can sometimes remove the crown, sometimes they can go through it, but this usually results in cracking of the crown and you will have to get a new one. See if your dentist can correct the bite again, sometimes it can take more than one adjustment. When your dentist says the tooth is in "bad shape" also ask him if it is able to support a crown for very long.
Occlusal interference may generate pulpitis like symptom. if your dentist can not adjust the bite optimally, you may need to see an occlusionist or prosthodontist.