Well, a main part of the tactic is pretty much: Use the Ashtar front ships to soak up all ordinance from the Vaegir and remain behind the main battle line of the Ashtar. Completely ignore the Vaegir in fact as they are not the objective. The objective right now is board, seize and jump out an Ashtar ship to a safe rendez-vous point and from there get the Ashtar ship to MSSC home space for examination. So to answer your question: They'll probably try to avoid being hit by your ordinance and not fire back at the Vaegir unless the Vaegir are threatening the success of the operation (in which case I'll either decide to pull my ships out before the damage is too costly or call in more support if the boarding is going really well and there is a real chance the MSSC can get the Ashtar ship. Mostly because I doubt my current fleet is capable of withstanding a full barage from the main battle fleet of the Vaegir).

Also, once the boarding starts, my guys will probably often call in precise dropship strikes on the boarded ship just to quickly dispatch hostiles.