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By all means yes, they should be allowed. I know this topic was being discussed last year, a few months after I returned from Iraq. There are a great many groups that fall under the umbrella of Paganism, just like there are many faith groups that fall under Christianity. There certainly are a decent amount of soldiers that I know of, some I know personally, that are pagans. The role of a chapalin is to provide spiritual support, moral guidance, being a source of confidentiality (except in very rare cases) and perform religious ceremonies. So there really is no reason there cannot be a Pagan chaplin.

Chaplains must both be an officer and be ordained (or equivalent thereof) in whatever faith they are a part of.

Neo-Pagan is more of a catch-all term for the various paganistic faiths that have arisen or been revived in recent years then an actual religion, far as I (or at least the military) can tell. It isn't the largest part of the services, but enough are in to have a few Chaplains in a recognized Pagan faith (ie Wicca), and the military does attempt to provide a place of worship for us, but again: Neo-Pagan isn't the largest, nor the most....united? organized? group of faiths around. This causes a bit of problem getting both services and Chaplains of the Neo-Pagan faiths.

Hopefully they can start to fill in that gap, though.

EDIT: Here's a paper on the Neo-Paganism and the Military. It concerns mostly Wiccan branch(s) of Neo-Pagan faiths, however it holds the same problems to gaining a Chaplin in the armed services as any other one. Witches 'n' Wizards 'n' Warriors, Oh My!