indyank - 5:55 am on Dec 19, 2010 (gmt 0)
Wheel, I guess the 5000 you are talking about is among the millions of pages you have...and I also assume that you get very minimal or nil traffc to those pages.But if they do have substantial links of their own, I will not loose them and they cannot be hurting your rankings.
Even otherwise, I am still not getting why should they hurt your rankings, though they are secondary.
Moreover, if you are getting minimal traffic to those pages, I am not sure why they should contribute to the load.
As for the options I do think loudly about two, though I would like other experts to comment on them.
1)301 all of them to the 20 odd pages - There will be some loss of link juice but a 301 of so many pages to a few shouldn't cause a problem in my opinion as they are all on the same domain.So, Google shouldn't be suspicious on them
2) spin off a subdomain for those pages and host them on another server.