The other options are unaware and impotent. I find these last two options far more likely. Yes, the head of the CIA 'answers' to the president, but the president isn't aware of every detail of every action the CIA takes. I'm sure his knowledge and direction is only at a high level. The fact is these institutions and their behavior do not change much if at all with the passing of each administration. This in itself says a lot.
The President, at this point, should not be unaware of the CIA spying on the Senate. We know it now, and we aren't privy to a daily classified briefing. So Obama no longer has this particular excuse.
As for impotent: if the CIA is operating independently of all three branches of Government, then it is operating outside of the Constitution of the United States. It is then the sworn duty of the President to address this issue.
If he is incapable of doing this duty, then we no longer live in a Constitutional Republic.
The duty of this nation's citizens would be, at this point, unpleasant to consider.
Those aren't the only possibilities.