Do Astroids give +1 defense die if the attacker is using Proton Torpedoes? I'm not very sure of this at all because it could go either way. I mean, the defender is still obstructed, but it seems like that rule is based on primary attacks.

The rulebook says the target rolls one more defense die when obstructed by an obstacle. I think it would be more specific if it applied only to primary attacks.

Yes, I would say torpedoes, and attacks of any kind, are affected by the "obstructed" rule.

Strategically, I would save my torpedoes in the event that an intervening asteroid is going to give my target more defensive dice. Wait for the clear shot at max range with a focus if possible.