I already tried moving the installation to root according to the guide you gave before. Unfortunately, something is truly screwed up. I can’t get the admin page (or anything other than the frontpage of the main site) to load.
It says in this part of the codex that I should be able to keep wp in its own folder and run in from the root directory, even with multisite. But it isn’t possible to follow the directions with the multisite dashboard.
Just wanted to confirm this issue and add that it also seems to prevent uploading new images through Nextgen. This happens even when not using Retina 2x on the Nextgen images (I use retina for other images on my site).