Yes you can! There is a recommendation that women with a diagnosed intrauterine infection during labor should not have their placentas encapsulated. A diagnosed intrauterine infection however is not necessarily synonymous with a fever.
A little known fact is that the epidural can cause a fever during labor. Also, if you do have a fever, has it been determined the infection is definitely in your uterus? What if you simply have a head cold virus?
A fever should not be a blanket recommendation not to encapsulate your placenta. If an intrauterine infection is suspected, be sure you get a definitive diagnosis if you really want to encapsulate.