I agree. My admiral will throw a tantrum when she sees her throphie literally evaporated. Also, yeah the 2 captured ones will have gotten away along side some shield tech which in the far future could serve as an shield bonus for my ships. Also some monitor tech (which is probably far less valuable than the shield tech). Also, you said SIF had the say through most of the ship. Would you mind if that meant that they knew where most rooms were so through 3D scanning and combat footage scientists could create a holographic structure of an Archangel's interior? So in future my ships would know what was where to hit it and boarding vessels know where to deploy the troops closest to rooms. 

Concidering the 2 captured Ashtar. I'd say that it's up to you when the knocked unconscious one wakes up (and when/if he commits suicide).

Last I'd say that some Soldiers died but all SIF (excluding Tanner who got shipped out in time).

Also I'd say I lost 2 Virtues and a Dominion due to the heavy blast and most of the sublight engines of the 2 Thrones would also be shredded.