Are you sure you still need the concepts of positive and negative energy? If so, make sure to remove any connotations of Good & Evil from them. I would just cut them out altogether along with alignment. It's used in a fairly confusing and inconsistent manner anyway (might improve in 3.5 though...)
I have no problem with a weapon that's Holy to one specific religion, and does extra damage to those opposing said religion (and/or to those that religion opposes - not necessarily the same thing!). Dealing damage to everyone not of the same fate might be overpowered though.
I have no problem with a weapon that's Holy to one specific religion, and does extra damage to those opposing said religion (and/or to those that religion opposes - not necessarily the same thing!). Dealing damage to everyone not of the same fate might be overpowered though.