Figured it out. Working too late, brain turned to mush.
Create a .maintenance file and upload to the root of your site, this file should contain minimally:
<?php $upgrading = time(); ?> <?php die(); ?>
You can include html to instruct site visitors to return later between those two lines.
You will not be able to log into site with this file present. Use an FTP client to fix any files affected. Remove file when clean files are put up.
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