That's a rough one, since the AI doesn't consider what is between it and its target, when on the attack. Your wingmen are always going to be perfectly willing to shoot through the cargo pods to get to the freighter, if that's the angle they're approaching at. You might consider having your wingmen tasked with dealing with the fighter escort (set to ignore the freighters), while Alpha 1 is tasked exclusively with destroying the Asmodeuses. Alternatively, you're left making the containers invulnerable after a certain threshold and hoping that the player perceives a challenge, even if one isn't present.
[edit]Leave it to me to miss the obvious solution.... Have the terran and vasudan wings launch their attack from below the convoy, or rotate the convoy ships, such that the friendly wings are approaching their underbellies. From that angle, they should hit the freighters without the cargo pods being in the way.[/edit]