Dead, diseased, or rubbing branches should be removed at any time of the year as soon as you see them. Pruning for form / aesthetic reasons can also really be done any time of year on a pomegranate, but the very best time is probably late winter to early spring. I limb my pomegranates up just a little bit (6" - 1' from ground level), when needed, so that I can get to the base easier and for better air flow at ground level. I leave at least 3 to 4 major stems/trunks per plant. Trunks will occasionally die back (especially during unusually cold winters), and, if you eliminate too many, the plant may be compromised.