No, the opposite is clear.
The ECHR court "found no basis that the case against the two was politically motivated, as Khodorkovsky and Lebedev alleged in their complaint" (direct quote).
The supra-national court is in no sense a pro-Russian organisation, and the judges were perfectly aware of the political implications of their ruling. They did note several improprieties of the trial (keeping defendants in cages etc.), and even ordered Russian state to pay some compensation to the defendants, but that did not change their core conclusion.
Khodorkovsky was enriching himself by defrauding the state and the Russian public (most of the social security is funded through oil taxes). This was the reason for his prosecution, regardless of what "everybody understands" thanks to various PR campaigns.