Which independent researchers did you have in mind? One example I can think of is in politically sensitive areas, where think-tanks bypass the peer-review process and try to get their "research" straight into media, through good connections. I think that is rightfully viewed with suspicion.

If your point was that researchers unaffiliated with universities have a harder time to get through the peer-review process - I don't think that's true at all. Often I do not even remember if a paper I read in the past came from a university or an industry lab. For example, in computer graphics, one of the most prolific institutions when it comes to publishing papers is Microsoft Research Asia.