David-
Then remove some sections.
A growing article with many stub sections should have those stubs removed then, so the TOC doesn't get in their way?
Stub sections are evil. They are a form of meta comment like "is this really true?" insertions in articles and should be avoided whenever possible. Wiki is a means to an end, not an end in itself -- Wikipedia is first and foremost an encyclopedia, not a scratchpad. If you want to talk about an article's potential future structure, use the talk page.
Articles should always be in a consistent state. Encarta or Britannica have many stubs, but they don't have "stub sections". In any case, I fail to see how the TOC can get in the way if there is no content it can get in the way of.
Then add some sections.
What if there is no good way to break up a few long sections into shorter ones?
Show me such a case and I will show you how it could be broken up. In any case, a TOC of 2 or 3 sections would only look out of place, and be of little help in navigating the article.
I agree than in an ideal Wikipedia, every article would have exactly the right number of sections of exactly the right length, and the TOC algorithm would word perfectly. But in the meantime, with a non-ideal Wikipedia, how can you defend the TOC feature's exacerbating the situation
Articles that have improper sections will be fixed sooner as the problems become more apparent. For example, I already noticed several articles that use colons in the headings. This looks very ugly, and the TOC makes it easy to detect such stylistic errors. Then, with the section editing enabled, you just select the heading, edit it, and save in a matter of a few seconds (OK, saving usually takes a while because of terrible code in that area).
Hiding our problems, on the other hand, will not make them go away. Those who are annoyed by the TOC can turn it off easily. But its current implementation should work well for articles that are reasonably structured.
Regards,
Erik