While it's easy to cry "conspiracy theory, everybody was in on it!" I generally believe the majority of these types of deaths, if they are actually shady, do not involve local law enforcement as co-conspirators whatsoever, regardless of the people who want to believe.
It seems that the upsides for actually following rabbit holes in these types of circumstances are little to none for local law enforcement. If you're a local law enforcement agency with little resources, what's a better outcome for the image of your agency? Take Occam's razor, even under suspicious circumstances, send the body to the morgue, and call it done, or send one of your detectives into the labyrinth?
Sending the detective into the labyrinth has two risks, both of which are bad. You'll either end up blowing a bunch of time on a conspiracy where one does not exist, or, in the case that there is, you will probably just end up sending a detective into a world of classified disaster and end up collateral damage of a much more powerful, much more insidious organization. Either way, probing further means you'll lose face. Most will choose the path of least resistance.