It seems that Gnome’s safely remove drive feature works just like the equivalent in Windows: not at all. It even displays the exact same useless error message, almost word for word: this device cannot be stopped. Not the slightest hint about why this might be the case.
Following this scenario, on Windows you’d pretty much be stuck shutting down your computer to be sure that no data loss will occur (although workarounds like Unlocker exist, or you can use Process Explorer to figure out the culprit manually). Luckily, on Linux the workaround is a lot easier. Use
mount to display information about all currently mounted file systems and
umount to, you guessed it, unmount the file system of your choice.
$ mount […] /dev/sde1 on /media/888E-E0E0 type vfat (rw,nosuid,nodev,uhelper=udisks,uid=1000,gid=1000,shortname=mixed,dmask=0077,utf8=1,showexec,flush) $ umount /dev/sde1
PS I just found out that I’m mistaken, but I already wrote the post and besides, the point that you’re able to do things like this if you want, whereas you’d be stuck in Windows, still stands. It seems that the way Gnome devs envisioned unmounting is not while you’re viewing it in Nautilus by right-clicking, but by right-clicking on the icon on the desktop.