There's not much you can do to hurt a juniper, other than spraying it with Roundup.
Yes, you can prune it to look like a bonsai (tree) safely. It's a matter of removing foliage from the trunk and larger branches to expose the bark, then shaping the remaining foliage in one of the bonsai styles. Which style to use depends on the shape of the juniper being used.
http://bonsaisite.com/techniq1.html