So they wouldn't flee with information. Also, to keep others in line, blaming their "usual suspect" just to show the people how "evil" he is, diverting people's attention away from internal problems. During the Iranian uprising the regime proved it had no problems with shooting its own people.
Pakistan foils planned jailbreak that would have freed Daniel Pearl's killer (Reuters)
from the article: Assassins of nuclear scientists are sending a double message to Iran