The problem isn't so much that Obama wanted the guy out. The issue is that it was done publicly and it was made known this is what the Administration wanted and got.
This will cause way more issues than just at GM. Obama is playing for a huge power grab that in essence is circumventing the balance of power in the government. People are seeing this and it is making them cautious as to where they put their money.
There are even Democrats, like Senator Byrd, that have gone on record saying this huge effort to grab more power by the President/White House is totally wrong.
http://www.politico.com/news/stories/0209/19303.html