Ubuntu :: Safest Way To Boot Users Off Of A Partition?

I need to run fsck on a large partition on my server on a periodic basis. In many cases, however, files are left open on the partition, e.g. XMing sessions are often left open for weeks at a time because connection is hit-or-miss, or jobs are left running.

My first thoughts are to shut down the daemons I know are using the partition, then traverse lsof for processes that have files open on the partition and do a SIGHUP, SIGTERM, SIGKILL sequence on them. One problem I see with this is that in some cases a script might be running a loop that performs a process on the partition. For example, suppose loop.sh is running from ~ and it loops process.sh over the files in /data (i.e. the partition in question.) The first signal would end process.sh, but loop.sh wouldn't be touched, which would allow it to proceed to the next iteration, etc. until the final instance of process.sh would get the SIGKILL and yet another iteration would start. Killing process groups might help here, however.

Ideally I would just go to init 1, check the filesytem (maybe run a backup,) then go back to init 4 (running Kubuntu, so no init 3.) I'm not exactly sure how to pull that off without the filesystem check happening every time the server goes to init 1, however.