Alan was happy to tell Dillenger about it. Afteral, on the surface, Encom was doing nothing illegal, so why would a security program be a problem right?
I'm sure on the surface TRON was seen as a way to make the Encom system more efficient. Dillenger could only smile as if all was good. To conplain or object would be to admit wrong doing.
And MCP or not, Dillenger was ultimately at fault. The MCP was, afteral, his ILLEGAL program. He was VP and all, but what he was doing was heading Encom towards being another Enron (hmmmm...) had he been caught.
So in summary, TRON was not an illegal program, just a system efficiency and safeguard program that Alan's bosses probably approved, and Dillenger was too busy running his illegal program to notice what was going on in the lower levels of the company... till it was too late.

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