My theory is that the extra entropy / noise / cognitive load of booting up yet another tool when you turn on your computer didn't match the gain in utility (productivity, etc.)
For both cases we used Slack, I agree with your assessment in that we used Slack JUST for IM. But if you already have Hangouts / Skype, what's the marginal gain from Slack? As OP points out, initially most people start using it for IM (as this is like muscle memory) but then channels grow, get out of hand, and someone needs to input effort to cut back the entropy.
But given the effort that knowledge workers put into email management, calendars, file management, etc. that's already a lot of cognitive load on controlling information entropy on a _daily_ basis. God forbid you work in Sales or something where you're in CRMs all day, and then you need to manage clients / contacts, or a Project Manager ... shit gets heavy quick. And that's all from doing stuff _about_ work, and not really working.
Another use case that's more microscopic to me: when searching for information in archives, it's easier / less stressful to have fewer places to search for files or conversations than more. Knowing that I only need to search my emails / IM/ files (or hell - if you use Google, it's ONE SEARCH BOX in Gmail for all of them!) is a tough hurdle to get over when you're trying to sell me Slack (unless you leverage their email add-in and send most of your emails / files to Slack, but that's a hard sell for any team.)