I'm not even really sure who your basic disagreement is with, I don't see where anyone claimed Heth is the unquestioned, unchallenged master of anything.
As to your list of "facts", the first three seem straightforward enough, though how you can leap from those simple ideas to an integrated view of the entire KK structure, how "purged" it currently is, how much resistance remains, and how long it can continue to resist before the "entire corporate structure comes down" is eluding me.
The one about the security forces, the very chron you linked went to great lengths to demonstrate that public perception is very much their currency and power, and Heth seems to have quite some aptitude at the public opinion thing. All 8 security services participated in the Caldari Prime operation, so even if unwilling, the megas can't seem to escape the public pressure that's been whipped up lest they be seen as aiding the enemy and made into the next scapegoats, which would be playing right into Heth's hands.
As to complicated, messy, and well told stories, first of all, again...how is this in any way lending to a "logical" understanding of a fictional construct? Second of all, every single one of those words is ambiguous and depends on the writer/reader.
Edit: Now, I'm totally on board with their being a great deal of conflict within KK as well as without, in the real world that might limit Heth's true ability for broad over-reach, but in a narrative its well within most people's suspension of disbelief.
I think we're just showing our inclinations on the whens and wheres of internal/external conflicts, overtness vs. subtlety, etc. :9