We're not discussing the true nature of ETAK, but rather Command's weird behavior towards Bosch and Iceni, which is of course related to ETAK and what Command thought it was.
Maybe command had a good idea of what ETAK was all along. ETAK was a project based on the GTI's research on Shivan specimens during the great war. Maybe the GTI actually discovered that the Shivans utilised a form of quantum pulses for communication. Seeing as how the GTI were eliminated that particular information would only be available to the highest ranking officers of the GTVA of which Bosch would've been before his little crusade.
I think GTVA command may have had at least some idea that ETAK was Shivan-related from the outset and that like the Hades rebellion ETAK and the NTF posed a dire threat to the Vasudans.
Here's some speculative mumbo jumbo that's got me thinking: what if Bosch was sympathetic to the GTI of the Hades rebellion i.e. destroying the Vasudans. Obviously he couldn't have been on the losing side of that conflict or else he wouldn't have been a GTVA admiral, but suppose for a moment that in plundering old GTI research into Shivans he started to agree with the pro-terran ideology of nullifying any alliance with the Vasudans only being the crazy megalomaniac he is he took it one step further and felt an alliance with the Shivans was in humanity's better interest.
In other words Bosch was the GTI hitting back from the grave.