I think the NTF are perfectly capable of taking out the fire control system on the Colossus for a short period of time, long enough for the Iceni to escape at least. After all, simply breaking the fire control system would be enough, it would still take at least a minute or two to get it back up or get backups on-line, even after minor damage.
I agree LS, the GTVI was seeing some useful research being done for them free of charge. It also makes sense to assume that the GTVI were aware of Bosch's intentions to open the Knossos portal before he actually did it, and I'm pretty sure they knew what was beyond it as well as he did.