What potential issues could arise when using a religious authority (for instance, the gods or God) as a basis for moral decision/justifyng a course of action?
Religious guidance in the form of holy books or even pastoral authority still requires a human interpretation, and that interpretation is imbedded in a social setting. For example, if you read “Thou shalt not kill” in the Bible, but you are a soldier (or a policeman), you have to filter the religious guidance through the social milieu. Another problem with religious authority is the “translation” from the original source to the current spokesperson (how’s your Aramaic?) But the most pressing need for something other than simple religious authority is personal responsibility for the consequences of your actions – we live in a physical world with “laws of physics” to obey; we have our “reason”, our ability to use logic to foretell consequences of our actions, and as social beings and as receptacles of “souls”, we must take responsibility for our actions. To justify everything based on organized beliefs is wrong-headed.
The greatest issue that would arise is this: for every religious authority used, there would be another (perhaps in another religion or part of the world) that preaches exactly the opposite. Both are right if used in the right contexts and both are wrong otherwise.
Moreover, unless the 'authority' is viewed as an IDEAL from every point of view - in perspective and in hindsight (with respect to the circumstance of use of the morality) - there is no point considering it without appearing hypocritical.
Along with the logic pointed out by Wordprof, one has to take into consideration that those who may be affected by an act based on religious authority may not believe in the same god/gods being utilized for justification. For example, an army of Christian soldiers might march upon the land of a Navajo tribe and tell them that by the authority of their god, it is their religious destiny to take the land from the Navajo and make it their own. The Navajo do not share this god, they know nothing of his alleged authority, and so to them there is no justification to allow a strange army to come take their land. Religious authority is all based on perception.