You have to keep in mind that we're dealing with Stalinist Russia here where you did what you were told or else.

I think what we're dealing with more is a former English naval intelligence officer's perception of Stalinist Russia, channelled through the thriller genre.

In real life, SMERSH was not nearly the kind of organisation it is painted as in Fleming. There were small groups of hunter-killer cells in the dying days of World War Two who combed through the DP camps assassinating traitors and others (ie Ukrainians, many of which were members of the SS units responsible for killing women and children). But the organisation had already disbanded by 1948, and even if you buy the story of it continuing regardless, there's no evidence they killed anyone at all. In reality, Le Chiffre would have been summoned to Paris or somewhere and put in a nasty little room and asked a lot of questions by SMERSH officers, and if found guilty, yes, packed away to Siberia. If you read the only serious memoir of anyone who worked for SMERSH - NIGHTS ARE LONGEST THERE - you'll soon revise your view of this organisation. It was feared, yes, but because they could send you to the gulag. The people who worked for it were almost to a man military desk men. It's much more similar to the work of the British in the London Cage than some kind of assasination agency.
The idea that Oborin (why not call him that?) wouldn't have countermanded his order for the reasons you state is, I'm sure, absolutely what Fleming was getting at, and in the context of the novel works. But in real life Oborin would not have been there, so would not have feared going to the gulag. SMERSH were the group who recommended sending people to the gulag, and that is what they would have done in this case with Le Chiffre.