To begin with, it's important to note that the Clu interrogated by the MCP in the original is NOT the same program seen in Tron Legacy. The original Clu was as you say - a "scout" program designed to find evidence within the ENCOM system that Dillinger had stolen Flynn's ideas. That version of CLU was destroyed.

After the events of the film, Flynn designed a much more advanced version of CLU to help him build his "perfect" world within the system. This CLU was a powerful AI program who was supposed to help control & fix the Tron world while Flynn was away. Unfortunately, CLU evolved to the point where his directives were open to his own interpretation. His ultimate motivation, however, was to fulfill his programming - to "fix" the world.