As a DM, I'd never allow it. Then again, as a DM I also removed the "have to be flat-footed" BS from Iajitsu Focus. The same reason applies to both, Iajitsu works uses physics to increase the speed of a strike made from a draw, thereby increasing the damage. You'd loose that speed benefit if you then threw the weapon (because it's from centrifugal force), but at the same time, whether or not the guy is expecting it ain't gonna make a difference.

Then again, in the OA game I ran, the Samurai/IM was preforming on par if not better than the Fire Shugenja in the party as far as raw damage output goes, so I don't see a need to "fix" Iajitsu Focus.