I have absolutely no problem publishing in a disciplinary journal with impact factor of 2-4. These are excellent journals, read by all active researchers in my field. It is bizarre to compare them unfavorably with Nature and Science, as if papers in a journal with an impact factor of 3 are hardly worth reading, much less writing.
This is entirely correct. Several of the key journals that I real all of the time are in this category: Pharmacoepidemiology and Drug Safety and Statistics in Medicine, to name a couple of obvious ones.
I think, to some extent, this is the dark side of a focus on impact. A finding that is of interest to a broad audience may not necessarily be a good measure of the importance of a finding to a sub-field. There are a lot of papers, to use an example, that say "further work in this direction looks challenging". This is important information to let other researchers know but it's likely to be heavily cited.
Now, there is a case to be made for the volume of research publications that are made being harder and harder to follow with time. But this can also be a benefit -- many clusters of researchers working in different directions may be able to better find optimal solutions that would otherwise be overlooked.
It is a complex issue but I'm definitely in favor of discipline specific publications and some of my favorite papers are in this type of niche.