Courage Points allow players to improve their test results (or avoid certain events or penalties), not improve initiative results. My first piece of advice is to stop allowing this player to spend courage on initiative.
However, even if you do allow it as a house rule, the player certainly is not spending her courage "heroically" every time she uses it. Or you could deliberately create scenarios where heroic spending of courage is simply not possible. Also, you may want to think about strictly limiting how fast she recovers them--like say after filling out lengthy reports to the captain about why she took out a room full of people.
Hope that helps!
LQ
Drunken DM and the Speak with Dead spell: "No, I'm not the limed-over skeleton of the abbot, and no this special key in my boney fingers does not open the door to the secret treasury! ... Oh crap."