'Innocent until proven guilty' also applies to governments and government organisations such as MI5.

So, there was this Ethiopian, who had had British residency but which had expired, Mohammed by name, who was in Afghanistan fighting (He says) against anti-Taliban forces (Who would they be, now?) and Pakistan and he was arrested by the Pakistanis who suspected him of being a terrorist. He claims to have been tortured by various groups, none of them British.

Have I understood this right?

This is somehow the fault of the British Government?
As I see it, HE is responsible for his behaviour, in Britain and in Afghanistan, and if his actions have consequences, then he should suffer them.