FSB could make him disappear (they could fake a botched kidnapping operation by CIA or FBI) and everyone will instantly suspect the Americans, and it will damage relations between US and EU countries.
Assange is just the poster child. He's not the phenomenon. Literally any college student has the tools to leak stuff to the Web in a way that will be difficult or impossible to suppress. Just post it all over. Stick it on Digg and Facebook, link to it on Twitter, upload it to a few filesharing networks. Wikileaks is helpful to a leaker because everything that appears there gets instantaneous publicity and a slew of immediate mirrors, which gives authorities a very short window within which to try and censor it. But Wikileaks is hardly essential, and Assange is even less so.
So turning the guy into a martyr is utterly counterproductive. That'll just spawn copycats. Angrier copycats. A better strategy is to make his life seem miserable. Just the total opposite of fun. Try to convince people that leaking stuff onto the net is a recipe for being slandered, being followed, and being subjected to endless, unglamorous, thoroughly unsexy bureaucratic harassment. One parking ticket per day for the rest of your life.
He will be dragged into court over and over. On the days when he isn't in court they will make him out to be a fugitive, forced to live in caves and avoid all his friends and loved ones. On the days when he is in court he will tend to look like either a criminal or a victim. None of this will stop Assange, of course, but Assange is powerless without the rest of the world: The people who are in a position to leak stuff to Wikileaks. They are the audience. And the message to them is: You can leak, sure, but you'll be found out, and then you'll either be arrested or be followed continuously for the rest of your life by men in black who are just waiting for you to slip up.
That one left me breathless. Surely no government would be that cruel.