https://core.trac.wordpress.org/ticket/42345
After a lot of digging and following segfaults in strace and parsing out apache core dumps (and enlisting some outside help from a much more knowledgeable Linux guy) I dug this up on WordPress’s site.
The short answer to the problem is that there is an issue with PHP5 and libssh2 that was introduced in an update a few months ago. There is no actual fix for it, but it can be effectively worked around by installing this plugin: https://wordpress.org/plugins/ssh-sftp-updater-support/
It worked like a charm for me; all my users can log in normally and I can once again update plugins and WP Core through the GUI.
Hope this works for you, and others!
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