Maybe he does understand how the Constitution works, however it appears that you do not. Congress has no authority to put anyone in jail, or hold criminal proceedings for anyone. (The absolute most they can do is hold him in inherent contempt, which cannot extend punishment past their own session. This has not been used in decades)
If they hold Rove in contempt of Congress, which is highly doubtful, then it will be kicked to the US Attorney... an Executive appointment, under the authority of the President. Given this, yes, it does matter what Obama has to say on the matter, and he says let it go.