No, that's not why Khodorkovsky ended up in prison. He gave money to Putin's opposition, that's why. As to taxes, its laughable, the ruling mafia in Russia steals $trillions from the till and not even trying to hide it.
Re-read what I said. Dude bought half the Duma by the time Putin went after him and was writing his own laws. And you're right about taxes, but do observe that taxes are only optional in Russia as long as you are an oligarch who doesn't have political ambitions. If you delude yourself into believing you can buy the parliament, they become very non-optional indeed. Selective application of justice can be a powerful thing.