"Future's End" showed a TIC officer attempting to destroy a starship on suspicion of its involvement in a disaster, guilty until proven innocent, with no attempt at due process.
That can be blamed on Braxton alone. He was obviously insane - suffering from the temporal equivalent of psychosis when he did this. Indeed, we would later learn exactly that.
As for "Relativity":
Ducane arresting Braxton for crimes he's going to commit...well, I chalked that up to an entirely new kind of criminal law having to be invented, to deal with a society like this which is so dependent on time travel. It may be incomprehensible and draconian to US, but not to them.
And besides, just how do we know exactly that the version of Braxton who is arrested, truly IS innocent? Of course he claimed to be. But who's to say that a search of his quarters didn't later turn up incriminating evidence? And since the Braxton who *was* a criminal was clearly showing signs of temporal psychosis, isn't it logical that the present Braxton also would be? (Remember, the later version of him did experience the events of "Relativity" that we see not-criminal Braxton do. So in a very real sense, not-criminal Braxton was destined to become criminal-Braxton.) Finally, I admit I'm a bit fuzzy on the details, but Braxton said that he was relieved of duty and forced to retire, but he did NOT spent a lengthy time in prison or anything like that. That would seem to indicate that the TIC is not quite as evil as they are made out to be.