The negative level only affects you as long as the weapon is in hand. Unless you are going to keep the weapon in your hand for over twenty four hours your ability to automatically remove the level does not come into play. Even if you did do that the second you no longer have the weapon in hand the negative level disappears. When you pick the weapon up again the countdown would start over again.
The description of the holy enchantment specifically states that the negative level cannot be overcome in any way while the weapon is wielded. Once you are no longer wielding the weapon the negative level goes away until the next time it is in your hand.
Resist Level Drain states that you don’t take any penalties from energy drain effects. Nothing in the description of the holy enchantment states it is an energy drain. Therefore you suffer the full penalty from the negative level. The fact that you can never die from the negative level bestowed by wielding the holy weapon is a good indication that it is in fact not an energy drain effect.
So basically you suffer the full effect of being an evil character using a holy weapon.