Assange is savvy enough to know their position inevitably supports Trump, but there isn't any reason to think if they viewed Trump as more corrupt they would be against him. So it is possible they take a principled position while wrongly accused of having a preference in who wins the election.
But very few observers of US politics believe Trump is the anti-corruption candidate. A more widely held belief is that he's the most corrupt major party nominee in the history of US politics.
Disclosure: I support neither candidate and will probably vote the Party for Socialism and Liberation this cycle.
Clinton's happens in secret and is masked by insincerity, lies, etc.
I think there's a brain glitch at play here -- corruption in the style of Clinton feels more corrupt because it's secretive, even if the out-in-the-open corruption is just as bad or worse.
Only this time, it seems the Clintons were trumped...
One possible explanation for this is that Assange will support the candidate that he believes will hurt US interests most.