It would be nice if there were a way to disable the hide all and show all options. While I'm sure it's a useful feature for the people who need it, it seems like it would have limited utility for most wikis. For now, I have edited out the appropriate code because on my wiki there is no reason to hide an entire article: it just makes the page pretty much blank, and the toggle text looks out of place on the expanded page.
Topic on Extension talk:SectionHide/Flow
I'll look at adding a configuration option, but it would be global (not sure how to do it per user, and per article means adding a magic word, I think)
Have you changed
$wgSectionHideShowtop = 0; //default
to 1? - this makes the hideall feature keep anything above the first heading visible. It was added for someone who wanted the option to hide everything but I realise now it should default to 1. I can add another option to disable the feature completely, but this may be all you need.
added check for = 0 so now if you set the $wgSectionHideShowtop to -1 it will not show at all