I'm no fan of Slack, but it has IRC and XMPP gateways. You can trivially set up an IRC bot that logs your channels & conversations, I connect to Slack via irssi & use its standard logging facility.
So you're no more likely to lose your logs via Slack than via IRC or XMPP if you set things up correctly.
How do you think open source projects have preserved message history on the existing open source alternatives discussed in this thread (IRC & Jabber)? You set up & maintain your own logging bots.
So you're no more likely to lose your logs via Slack than via IRC or XMPP if you set things up correctly.