Au contraire: I think the metaphor fits perfectly in both directions. That's why I chose it.

Ideally, your self-defense systems only attack those that are actual "invaders" but if something looks/smells/acts like an invader, it gets attacked as well, even if it's really not "harmful."

Believe me when I say I'm sympathetic to the argument that the security apparatus has started to attack "healthy tissue" (to extend the metaphor) but the alternative can't be no immune system.

It has to be better, more appropriate, more selective, and more effective.

To continue the metaphor, I believe both immune systems mentioned perform necessary functions. As a side note, the parts of said immune system responsible for investigating pollution and white collar crime could do with some strengthening.

However, states are better understood as highly symbiotic ecosystems. This is more pronounced in third world states, where the military , intelligence agencies and political leadership form distinct power blocks. In the US, some hypothetical power blocks are the military-industrial complex, the alliance of media companies pushing for maximal copyright combined with the regulatory apparatuses they've co-opted, and Fundamentalist Christians, and the various three letter agencies with their constellations of contractors.