I think it might be a better idea if they err more along the lines of too hard to dodge rather than too easy. Could you, say, send in a sacrificial fighter to detonate the torpedo if you can't shoot it down or dodge? Maybe all you need is a little micro.
Why a fighter? Wouldn't a group of Missile Frigates work? Or are the torpedoes smart enough to avoid detonating on things they can't AOE?
I haven't used Torpedo Frigates or encountered them in AI hands yet, so I don't know and have no game experiment with.