Greetings, all! Based on preliminary testing, alignment-based weaponry (Axiomatic, Anarchic, Holy, and Unholy) weapons do not bestow any negative levels upon their wielder, regardless of alignment. (In tabletop, a character of opposing alignment, like a Lawful Good character wielding an +1 Anarchic Crossbow, would get a negative level.) This is contrary to tabletop. (Holy Weapon Property - Example) This means you can have CG characters in your party wielding Scather and +1 Holy Axiomatic weapons at the same time with no ill effects! Please confirm or deny from other sources.
How are you checking if the negative level has been applied? I believe if you equip and then unequip you will notice a difference in your HP max. It will not tell you "Negative Level Applied".
I was using first level characters to hold alignment-based weapons who got access to these weapons due to party members crafting them. (The crafters used console commands to level them up.) I didn't see any HP reduction for the level 1 lad, nor was he instantly slain as I expected.
I tested quickly with the Holy ranseur. I used console to change my alignment to Evil: the HP decreased by 5; Saves and Attack decreased by 1. However, I did not lose one slot of highest memorized Wizard spells as it should. Possibly because I have one level of Ranger and it ''removes'' a slot from my empty Ranger spell list?
Try it with 2nd level characters, and check the max hit points. I suspect trying to apply a negative level to a 1st level character might have no effect.
When I equip the Holy ranseur on an Evil 1st level character they die (HP goes to -10). I didn't check with other alignment-based enhancement, but it should do the same. The item has to be equipped, not just held in the inventory by the way.