After reviewing the episode, I have three theories:
Crime Cannot Pay
Batman is a firm believer in moving within the limits of the law. He repeatedly offered Clayface a chance to have a lawful cure, and could not countenance the cure being done with stolen materials and kidnapped doctors. It was the method, not the cure, that he opposed.
The "cure" was untested
The FDA clamps down on people preaching wonder cures involving everything from injected stem cells to lethal doses of belladonna to bleach enemas. They do this because these "cures" typically involve a small sample size and erasure of the failure cases to make results look more impressive. There was no guarantee that this would have actually worked for Clayface. In fact, the fact that Clayface seemed to be falling apart even faster after the partial injection suggests that it might have "fixed" him in the same way that methamphetamine "gives you more energy", namely that it overcharges the system, giving him temporary control, but ultimately leaves him more damaged. In a more clinical setting, this effect might be better controlled.
It would not have made him "normal"
Lastly, addressing your point about it being easier to capture Clayface without his powers... what makes you think it would make his powers go away? All that is shown was that it allowed him to hold a human form longer. Odds are, he still would have had all of his prior powers, just with more power and control, something which would not make him easier to catch, and would not fix his base psychosis.
