Maybe Brena was playing a Kira Yamato by just disabling the enemy instead of killing them
I know Brena will be Alto archnemesis simply cause they are firing at each other at the opening credits, hehehe
the VF-27 must have active stealth, since noone notice they were around and it was so easily hidden, perhaps the VF-27 is special ops valk and Brenas orders were to infiltrate a Vajra capital ship and gather as much data possible, hence the NUNS dude satisfaction for a Vajra capital ship showing up, and perhaps Brena fired at Alto since his actions could jeopardize his covert mission and when he noticed the Quarter pounder coming he had no choice to bug out since the ship would go boom boom either way...
just my crazy assumption so far, hehehe