Personally, I think these kinds of self restrictions should correspond with whether or not you respect said enemy or have your own set of moral/ethical codes of conduct.
From a practicality standpoint, however, I tend to agree with the words of Machiavelli. Here's a particularly relevant quote of his:
Niccolo Machiavelli said:
Men ought either to be indulged or utterly destroyed, for if you merely offend them they take vengeance, but if you injure them greatly they are unable to retaliate, so that the injury done to a man ought to be such that vengeance cannot be feared.
If you're going to destroy your rivals, you shouldn't do a half-assed job. Once started, you must destroy everything they own and care about. Don't give them the opportunity to seek revenge.
Edit:
Merkavar said:
on the same line of thinking, opening fire on a church or other similar building. im not religious but it just seems wrong too. also it wont help you win any hearts, minds or support opening fire on churches or funerals.
During World War II, German-held towns and villages often had snipers and artillery forward observers posted in the steeples of churches. This kind of thing happened so frequently that, almost as a rule, allied forces would open fire at them when laying siege to Nazi occupied areas. Following your line of reasoning, I'd hate to be the CO in charge writing a heartfelt letter to Little Jimmy's parents about how the top half of their son's head was blown off by an anti-tank rifle because "it was against my moral code to fire at a church full of Nazi snipers".
((Godwin's Law strikes again!))