I think you mis-read D3.1. 
This is usually applied to an individual race in which the incident occurred - having half a race win deducted from their score means you generally don't have a tie to deal with and is punishment enough.
In the knock out stages it may mean that they don't get to the required number of wins, so the other team gets a chance to come back - one of the reasons for saying "first to two wins" rather than "best of three"
 If you ever deducted half of their total race wins it would be the equivalent of throwing them out of the regatta and would probably be a rule 69 incident.

Needs  re-wording, then.
Perhaps:
"Half or more race win" (singular) if a limit of one win penalty is meant.
"Not less than half of one race win" if no limit is intended.

It doesn't need re-wording, as I said usually, this wording leaves open other possibilities.

There might be circumstances when the umpires might want to apply a penalty of more than one race win. You never know the circumstances until they happen.

Thanks all for the prompt replies. 
I'll code my system to be flexible given the above. Including scoring -0.5, -1, or -"Whatever" for a particular race.
I'm glad i asked.

I think the wording could be clearer Nigel. Better in my view would be "half a race win or more may be deducted" - a small change that would in my view make this unambiguous.

If you are coding this, the penalty is applied to total score, not an individual race.  I.e. if the boat goes 5-3 in the round robin then they still earned 5 points.  The penalty is a deduction from the total number of points earned and is usually shown as a separate column between the earned points and the final points.  Obviously, you would need to allow multiple penalty deductions to be applied/entered.