My thoughts reading the paper were always "how could they not shoot this down?" The pressure on journalists has grown tremendously under Putin, and the authorities were clamping down on anything remotely resembling subversion. Even if the authorities did not exert direct pressure, most publications would self-censor in the fear that the security services would go after them next.
How the Exile was allowed to continue is beyond me? But judging from my wife's magazine's intrepid reporting (published in Russia under the auspices of Ria Novosti - the State news beast), the English language publications generally pass under radar. She's never felt any pressure direct or otherwise to pull or amend critical stories.
It's important to keep in mind that English language publications are a drop in a bucket in Russia where I would say less 5% of the population can read and understand English. It simply has zero impact on the public opinion domestically, but it does wonders "exposing" the truth to the west, while showing how unfettered the press is in Russia. It's just not the mainstream press we are talking about here.