Um guys, the "intelligence community" did Trump a huge favor by getting rid of Flynn. The guy was trouble, would have inevitably melted down, and by getting him out as soon as possible and as far from any election as possible, it means he does the least possible damage to Trump. If they really wanted to hurt Trump, they would have kept him on until, oh, 11 days before the 2018 elections.
They weren't trying to do Trump a favor, they were simply looking out for their self-interest. Flynn could've potentially been a danger to their personnel and their mission of serving the country. I also doubt they prefer one party over another and, if they do, their preference is likely for Republicans. The problem is solely Trump and the faction within his administration associated with Bannon.