I wouldn't think so.
The ability targets an enemy. So the effect is on the enemy targeted, not your weapon. Your attacks against the enemy bypass any Damage Reduction and Energy Resistance of the target as though it had the listed weapon fusion. The weapon does not actually gain the weapon fusion or any other benefit.
As a move action, you can spend 1 Resolve Point to pronounce a creature you can see an enemy of your faith. Until the target is dead or the next time you take a full 8-hour rest, all your weapon attacks bypass that target’s DR and ignore its energy resistances as though your weapons had the fusion corresponding to your chosen alignment (even if the target isn’t a dragon or outsider): anarchic (chaos), axiomatic (law), holy (good), or unholy (evil).
I'd definitely have to agree with breithauptclan. That ability does not actually say that you treat your weapon as though it has a fusion.
On the other hand, I can't think of many cases where that would be a big lack, unless you were a level 4 character who only had nonmagical kinetic weapons (which would be a weird decision) and either attacking an incorporeal foe, or trying to use the ability to bypass DR/magic on an enemy that doesn't meet the alignment requirements.