I think we may have a difference of opinion here... 
Besides. My outrageous claims are partly hypotetical. With the without the Shivans and all that... Bosch was mostly just after the Shivans. Without the Knossos to divide his attention, and the ultimate mad dash to it, the rebellion would have dragged on. For years maybe...
Okay, let me recap some things for you.
"Command? Where's the blockade? Why isn't the alliance guarding this node?"
"I regret to inform you that your efferts to intercept us have failed pilots. You would be well advised to question the wisdom of your leaders. Helm, engage subspace drive"
So. Command traded Bosch withdrawing his forces from Deneb for his unfettered access to the Sirius jump node.
The only reason for you to see that, was for something that would happen later, which you would be able to figure out from his monologues.
Fast foward to King's Gambit. You enter the field of engagement precisely at the time for the re-initiantion jumps of the NTF capital ships. Orions, Deimos', Aeolus', you name it, it jumped in. You nuke it all, and Command knows exactly no more are coming, time for you to go somewhere else.
Enter Sicilian Defense - now, right here you should've heard something familiar.
"Command? I've got a visual on the Vindicator, but the Iceni is nowhere to be found. Either recon screwed up, or Bosch jumped already. Should we abort?"
Of course, you do not abort, you destroy the second Orion, and then you pound the ass of some other nice ships that jump in, a Deimos, etc. etc. and then it's time to go to the gate.
Come Endgame, few more ships jump in that the Colossus is more than ready to dispatch, and then BAM, HERE COMES THE ENTIRE REASON FOR THE PAST THREE MISSIONS! Uh oh? What's that? Guns don't work? DAYUM!
Now, I believe Goober was the first to point out (some of us knew it already but never talked about it, I personally figured it was obvious as hell) that of course, there was no sabotage on the Colossus, it was the GTVI that let Bosch go by. After all, it makes sense that you wouldn't want to destroy the Iceni, you would want to board it and take ETAK, considering how it is the focal point of the entire reason the NTF exists.
However, for those of us who are good at solving puzzles, you can clearly see from the setup of these few missions when you're with the 64th Raptors, what exactly happened, through the Bosch monologues when he talks about the NTF being stupid cattle, etc. etc.
See, what happened wasn't that the GTVI let Iceni jump, as much as it was another trade. First, Bosch sacrificed his forces in Deneb for his unfettered access to the Sirius jump node, and here, he basically sacrificed the bulk of his NTF fleet for clear passage to and across the Knossos. He gave the GTVA the exact time those ships would be coming out of the nodes (after he had ordered the NTF ships to go through those nodes) and for letting the GTVA take care of their inhouse traitors, he was given free passage to continue his ETAK project at his own expense.
You will note throughout the entire game that is Freespace 2, that Bosch succeeds at EVERYTHING he sets out to do. EVERYTHING. This is the reason he gets his own monologues. From activating the portal, to making friends with the Shivans. What the Shivan intentions are, we will never know, however what we do know is that Bosch did go to whatever the Shivans call "home" (in this, our, universe anyway). We know this, because the only reason we ever found the second Knossos in that huge nebula, was because recon tracked the Azrael transport that carried Bosch to it, and the Azrael jumped to the binary system beyond, which means Bosch was heading to places no other man has, as in, the Shivans let him go beyond. The sign of a good strategist, and therefore Admiral, is to know when to trade your chess pieces (and for what to trade them for) to achieve your objective. He traded his assets perfectly to achieve his "joy". Traded in everyone at the NTF, even the crew of the Iceni in the end, to get his way.
Coming back to what destoryed the NTF - Bosch did. You were just there at the right time to get your medals. Thinking you had anything to do with it though, is just a fairy tale. It was Bosch who created the NTF by playing to the retards fears, and it was Bosch that ended the NTF by trading them in for his true objective. See, this is one of the reasons Freespace 2 is such a good game.