However they're clad/armored, Andy's right. There would definitely be a dark secret. Speaking of which, the U.S. has had its share of dark secrets, and we've got a free press and democratic values (if not democracy itself). Just imagine how many dark secrets the Imperium would have.
The United States has backed coups and military dictatorships all over the world (Argentina, Chile, Guatemala, Iran, and Vietnam, just to name a few off the top of my head). And we're the so-called land of the free. So the idea that the Imperium, a hereditary monarchy, might do this on an even larger scale is... well... it's so obvious, it should really go without saying (IMHO).
However, I like the shield of plausible deniability that "Real Power is Local Power" implies. Instead of the Emperor being responsible for the bun-buns, it's Count von Nimh, Supreme Field Marshal of the Coreward Defense Forces, obviously somebody high-up in the establishment, but low enough to give even the Archduke plausible deniability if/when the whole thing goes public.
I guess my basic point is that people are bad (but have been largely tamed by society), organizations are worse (they have greater power than individuals, so they can get away with a lot more), governments are evil, and, finally, big, powerful, hegemonic governments are essentially chaotic evil. I admit, it's a peculiar worldview, and if you don't share it, I totally understand, but it's why I believe that any human government as powerful as the Imperium would not be benign/hands-off, at least not over the long run. But YMMV.