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Well, it being the rules forum, I looking for the rule... personally, I'd be hard-pressed to allow it, but certain character who gain benefits from it (Justicar, Vow of Peace), I might allow it.
Well, I'm apparantly gonna answer my own question... the exalted feat Holy Subdual will convert holy bonus damage into nonlethal damage, implying it couldn't be chosen voluntarily without the feat.
You could do nonlethal damage with the weapon and the extra damage from energy would do regular damage. This might be perferable sometimes
There is also a subdual enhancement that turns all of the weapons damage into subdual. That would definately change all of it to subdual. Although I have heard some people say it is too strong..lol