The latter makes it sure that the GTVA didn't know about what ETAK is at this point of the campaign. Thus we must say that they still think that ETAK is a weapon (if they know what it is, then the obvious question is: who gave the info? /I'd say Bosch/). If so, GTVA would surely decide that destroying the Iceni - thus slashing the dragon's head - is more useful than searching for a superweapon.
The question is: why didn't they do that? Because Bosch was their agent.
Uh no. What about SOC's undercover agents hearing rumours here and there and ETAK, perhaps NTF pilots re-defecting to the GTVA? There are more possibilities than Bosch informing the GTVA about ETAK.
And as for not destroying the Iceni - on that frigate holds the full research and information about ETAK. The GTVA wants the information so if they destroy the Iceni they would lose the only source of true information about ETAK.
Finally the question is - if Bosch really was a GTVA agent, with such power over the NTF, why didn't he just beam over the specifications of ETAK? Why didn't he just stop when the Colossus blockaded the Knossos portal?
It would be nice if you'd at least TRY to think that this is true, thus you'd be able to answer these questions on your own.
1) If there are re-defecting pilots, then it's sure that they're coming from the lower ranks, thus they don't know what ETAK exactly is.
2) As I said it earlier: why is the GTVA so interested in a superweapon? Considering the rebellion, it would've been much more useful to deal with Bosch - thus slaying the dragon's head. And, as I proved it earlier, GTVA doesn't know what ETAK is at that point.
3) The SOC mission was a ruse. A RUSE. And nothing more, OK? I'd say that it was forced by people who didn't know about Bosch's real belonging. Trust me, if the GTVA would've wanted this info that much, they would've just captured the Iceni outright. And if they know that this "weapon" isn't done yet, we can ask again: What is the source of that (nonexistent) information?
4) Why didn't Bosch stop? For the Holy God's sake! He had to test the device!
By the way, this point of yours made me think and I took a look on that "NTF saboteurs" on the Colly.
30,000 chosen crew members. Including NTF loyalists? Come on! It is sure that there was a strong security protocol on the Colly and it is highly improbable that they were able to get over there. If they were NTF loyalists (note that the Colly wasn't done before the rebellion started), then why didn't they defect earlier? Did they decided that "Oh my God, there might be a big bad GTVA ship, we should wait that if it exists, we should get up and sabotage it if attacks the good old Iceni?"
I'd say that this is another occasion of the GTA helping Bosch: letting him through the Knossos.