Here's what the weapon can do if it has dominance and is upset with you:
- Force its possessor into combat.
- Refuse to strike opponents.
- Strike at its wielder or her associates.
- Force its possessor to surrender to an opponent.
- Cause itself to drop from the character’s grasp.
Intelligent weapons will typically make demands of the wielder first, and then use these measures if that doesn't work. However, they are intelligent items, and they can go a more subtle route if they want.
But as Cthulhu says, even if the weapon does somehow take control of you and make you perform an evil act (or performs an evil act while in your hands), you won't actually change alignment, since you didn't willingly violate your god's ethos. You may still need an atonement spell, but as I said earlier, it shouldn't be too difficult to receive one.