It is similar to your option 4, while reasoning may differ to a degree

Antimagic ray doesn't affect objects, but it affects effects, created by those objects.

+2 enhancement bonus is not an effect, or it is not an effect, which affects the target of antimagic ray. It works, as well as any effect, which affect weapon wielder or weapon itself.

Fire damage, casedcaused by flaming weapon special quality is spell or spell-like effect, which affects the target of antimagic ray. So, it doesn't happen.