Attacking the Pope is a surefire way to get excommunicated. What? Aren't you Christian enough to know that Thou shalt not attack thy Holy Father ??
NB. In that case it doesn't matter if you were defending the territory or not. You are dealing with an ambitious Pope directly, not with another Catholic faction. He makes the rules, he can bend them, you know?
Kill him quick or ask for ceasefire after the siege ended.