What you've described makes sense logically, but yes, it's definitely not ideal. I've been thinking about the reindexing/rebuilding process a little lately (for Flying Sphinx, but the idea fits more broadly as well), where indexing happens in a separate location, and then the new files are brought across with .new. added before the file extension, and the live index set is rotated.
This would avoid the problem you're facing, but it's just a matter of managing the entire process (more moving parts = more complexity to manage = greater potential for bugs and odd edge-cases).
If you're particularly keen to see this change in place, can you log a ticket on GitHub, and then I've got something to keep it in my head :)
--
Pat
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https://github.com/pat/thinking-sphinx/issues/522