Yeah, I subscribe to your assessment here. It seems like a thrown thread in there, hinting right at your paranoia gland that goes nowhere apart from that exception in Flaming Sword that you mention, and another one, much more important.
Before that, let's realise that in SOC loop 1, where you infiltrate the NTF, all Command actions are correct and ethical, in a narrative context where they could well have chosen to reveal a darker, fast and loose side to GTVA's activities.
The other exception is the incompetence of Command to capture the Iceni in all occasions, with infiltrators even capable of disabling momentarily the Collossus so that Iceni can escape to the nebula. It's more than suggestive that Command did let Bosch escape on purpose, they were aware of these sabotage attempts and they let them perform it so that Bosch could end his project's mission of contacting the shivans. As a guinea pig, Bosch was the perfect sample, extremely intelligent and resourceful, and 100% expendable. Let him go to the shivans, watch his experience and oh, what a pity, he died horribly by the shivans (or something else, an open thread to FS3, surely), nothing lost here.