There may be a more complicated reason, but not all free agent signings result in compensation. For example, when Waite left Carlton for North as a free agent, Carlton were not compensated.
Freo would need to table an offer to Clarke in order to even have a chance at compensation. I'm not sure what the minimum permissible offer is (my guess is the AFLPA has a listed veteran's minimum in their collective bargaining agreement) but perhaps Freo were worried that Clarke would take any offer and therefore be paid to take occupy a list spot. If there is only a small chance of compensation, then it's probably not worth the risk.