The Lost Fleet/WMG

The Syndics gifts in the first book were real

 * The reason the merchant shuttles were staffed with sailors was because the merchants had refused to do it. The ships weren't booby-trapped, and Geary made a mistake when he demanded gifts from the Syndics and then refused to accept them because he was paranoid. The sailors posing as merchants thought it was a suicide mission since they expected the Alliance to take them prisoner, and then deal with them the way they used to do.
 * Have to re-read it, but didn't the ships go to full acceleration when the Alliance tried to brake via remote control? And then they simply changed the course to aim the ships back at the Syndics?

The unforgivable thing mentioned under noodle incident was a zombie/reanimation program

 * Think about it. The Alliance worships their ancestors, and to reanimate corpses to fight would probably count as sacrilege. Reanimating a human with memories and personality and all would mean stealing their souls back from the Living Stars, and reanimating them as a non-conscious zombie is at its best disrespectful towards the person that once inhabited the body in question.
 * Alternatively, they invented brain uploading, preventing the soul from ever reaching its ancestors.