The advantage of a same-filesystem move (usually to a subdir or alternate directory) is that it's a fast action. You're renaming an inode, not copying data around. When you're dealing with many, or large, files, that's an issue.

(Assuming Linux) If you're concerned with open files, you can do an 'lsof' and screen for files of interest. 'fuser -v filename' will show the process using a file, 'fuser -vk filename' will kill it (xargs or loops for many files, obviously).

And not everything that you're cleaning up is necessarily files, so adapt methods accordingly.