What appears to be a long jump to a non-expert on first glance, on deeper inspection will usually turn out to have involved multiple small incremental steps culminating a final discovery. Since we have to acknowledge somebody we usually pick the guy/gal who finished the job. I'm not saying that all work is equal, but imho planning for long jumps is impossible (it's not like researchers don't want to make big leaps in understanding).
Examples which have changed my mind about this: Andrew Wiles' Fermat proof, evolution of RISC, quantum theories. I am pretty sure that if I dig into it, I'll find that relativity and evolution also built upon previous work.
You are 100% on point.
The parent's poster's point on conformity is well taken. Still, "independent" researchers are viewed with suspicion because research is hard. As psranga points out, to make a long jump a researcher has to stay on top of the incremental steps. Unfortunately, for 99.9% of people, to do this they must be fluent with the literature and much more importantly talk with other researchers. No one works in a vacuum (and don't bother bringing up counter examples like einstein or newton).
Conformity is a big problem. It might arise when too many PhDs are hustling for a small pie. I'm not sure.
What was the big heresy for one generation changes into "what you have to say to get tenure" in another.
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.
That's not to say that academia isn't horribly broken, it is, but in some places it really seems like the author is going off in the wrong direction.