I've been doing a bit more research on this and can reveal the following.
I do an early morning 'speed origami' class before work, which is also attended by Michael Brooks (he used to make these cool paper Sidewinders and Cobras, but now just seems to leave little paper dinosaurs all over the place). This morning I asked him about Commander Thrust and this is what he told me.
Thrust was a well-known player in the betas, but was becoming more and more disenchanted as time went on. He started messing around with the back-end files and stumbled upon the original iteration of the AI written by Sarah Jane Avory. This original version had to be stopped as it came under the scrutiny of the security services of the USA, China, Russia and Mozambique. But thrust was able to download a copy and modify it. He decided to unleash the nascent AI back on Frontier. But he had read enough Sci-Fi about AI, the Quickening and Singularities to know how dangerous it might be, so limited it to the forums. He also gave it elevated permissions. FDEV soon discovered what had happened and banned Commander Thrust. However, it was not a full IP block, so he was able to start a fresh account following the game's launch and has been playing under a different name, and is very active on the forums under a different name.
As for the AI, Frontier where unable to remove it. However, it is constrained to the forums, which has stopped it from taking over the world. It is still here now.
The AI was code named 'Turing Junior'.