Okay, got it! I have to say, I've never heard the term "native search" before. I thought that's what you meant from context, but just wanted to be sure.
Glad to hear they aren't pushing to change the URLs, which would be incredibly stupid, but it wouldn't be the first time...
Anyway, would they go for a hybrid strategy that would llok like this: directory page has a nice H2 title for the summary of each of the pillar content articles, and then a section labelled "More on blue widgets" that would list say your ten highest-ranking, top traffic pages. At least then you would keep those only two hops from the front page and get them in front of the eyes of visitors.
Then perhaps it would have a link at the end of the list saying "See the full archive of blue widget articles" and it would link to some sort of index page, or some such. I don't know how many main topic pages you have and how many pages per topic you have, but you might have to think through your information architecture partly with an eye towards some sort of balance there.
I think whatever you do, you want some good internal links, perhaps with a variety of anchor texts, pointing at least to your high-ranking articles to keep them crawled and in the fore and passing link juice.
That said, it sounds like they're watching this from an intelligent business perspective: traffic that doesn't convert is a *cost* not a *revenue* and so if these pages truly convert poorly and divert sales, it sounds like they're taking a good approach.
It may be in the end that you want to sacrifice some high-ranking low-conversion pages and have them way out in the archives, but linking back rather directly to the key conversion pages, while the key conversion pages link to the high traffic pages by a series of hops. That may, over time, impact the rankings of those pages, but since they are a cost and not a revenue source, that shouldn't be a problem as long as you keep working on the site and getting the conversion pages to rank well.
Just my $0.02