There is no precedent. Teams allow employees to take promotions. They expect compensation for lateral movement. Ozzie going from manager of the White Sox to Marlins? Compensation is expected.
Theo is taking a promotion. Unless it's to a division rival you allow them to move on. You don't see compensation for guys going from bench coach to manager, assistant GM to GM, or GM to president. Theo has done a lot for Boston. Why they tried to get in his way is beyond me. Theo is now President of the Cubs. The new GM is Jed Hoyer. The Padres deserve compensation because it's a lateral movement. The precedent set by Ozzie would apply.
Also Boston has asked for better prospects than those given up by the Marlins. They wanted guys like Brett Jackson and Trey McNutt.