Then, the GTVA (or rather, some faction inside it) is working for Bosch.
Bosch (and perhaps his co-pilots, but they are not montioned) found out things that GTI people were working on; GTVA buried them but didn't bury Bosch. So, perhaps there were other people like Bosch, who knew something about the Shivans that GTVA command was not willing to give into public? And perhaps these people were sympathetic to Bosch's cause (not the xenophobic movement, but the communicating with Shivans -thing)? It's possible there were more people in GTVA with similar records wih mr. Bosch: fought in GTI rebellion, found out something (what, we can again just guess), got themselves into positions of some influence, like admirals or generals and stuff like that.
Why did the Command let Bosch escape? Without giving reasons on or off the record? Any way, there definitely is something fishy about Bosch, and his Shivan-related activities, and the open plot lines do suggest that a sequel would have told us more about it, but it seems it never will do that now.
...does anyone else find it disturbing that we're debating of wheter or not there was some kind of a conspiracy going on in a fictional universe? Bah, perhaps there were no conspiracy, just spies giving bogus co-ordinates and conjuring sabotage on fire control systems of cap ships and stuff like that. But then again, you'd have to discredit the GTVI for not finding out and thwarting these counter-covert operations, if that's even a word.