We are told that to destroy Clu, Flynn must undergo "reintegration", which would destroy Flynn as well. Likely that was equally true for Clu; to destroy Flynn, Clu might have had to destroy himself.
Other possible reasons:
- Without his disc, Flynn was irrelevant.
- Clu is programmed in such a way that he is forbidden from directly harming Flynn.
- Clu's goal was to escape the Grid. With that done, Flynn's destruction would be easy. (Just a keystroke, as they say...)