Don't be ridiculous... Disbanding of Imperial Intelligence does not fall under "day-to-day running". The Imperial Intelligence is what basically keeps the Empire together and is parallel in importance to Imperial Military (which is pretty much the most important element of Empire). If Emperor or DC wouldn't care about that then they wouldn't care about Empire at all. It is true that Emperor had bigger goals than the Empire (JK storyline) but the Empire was the only mean to achieve that goal. So if the Empire would collapse from within as a consequence of disbandment of Imperial Intelligence then he can kiss his goal good bye.
The knight story takes place before the agent and warrior stories, therefore what you're saying is immaterial in ways that i won't go into because this thread isn't marked of knight spoilers, but are pretty obvious to those who've played the knight and warrior stories.