I don't know the pinout on a CF card, but my guess is that the broken pin is supposed to be a spacer intended to prevent inserting the card upside down. My own CF reader has an extra long pin in that location.
If my guess is correct, you'll be fine as long as you always insert the CF card the correct side up (whichever that is). If you do happen to insert it the wrong way, serious mischief might result, or perhaps nothing at all.
Eric