Because Taiwanese businessmen shirk their social, ethical and legal obligations to their workers by fleeing to the self-governed island, and the rest of China has no de facto authority over them. Beijing must be able to send in its police to find violators of legal obligations and deal justice where it can.
After accumulating massive debt and back-pay obligations, these businessmen quickly escape and effectively leave their problems for the locals to solve. Essentially with no legal influence over the residents of that selfish island, the businessmen who come to China to do business assume no risks--if things start to falter, run away.
Even when Latin America couldn't or wouldn't pay up its debts America intervened (Roosevelt Corollary). Even if the Taiwanese assume themselves independent, China should enforce legal obligations.
Germany would happily cooperate with US officials should any German businessman try to escape his obligations. Taiwan should cooperate with its Mainland counterpart, too. Either that or enforce the March 2005 doctrine, Beijing--capitalism and social stability ("the harmonious society" in Hu's words) are is at stake. At a time of economic uncertainty, the poorest ranks of the developing world--the working class--cannot afford to not have the pay and severance they worked for and earned.
Let's not set a massive precedent for risk-less foreign investment at the cost of those who represent the bulk of China's citizenry: the workers.
(In theory it should also work if the ROC government controlled the rest of China too, which is what President Ma says is the case, as long as there's a single legal entity to enforce contracts and obligations)