http://sphinxsearch.com/docs/latest/rt-caveats.html
"In case of a damaged binlog, recovery will stop on the first damaged transaction, even though it's technically possible to keep looking further for subsequent undamaged transactions, and recover those. This mid-file damage case (due to flaky HDD/CDD/tape?) is supposed to be extremely rare, though."
Not even the developers of Sphinx know exactly what the problem is, but at least we know now that it IS an internal Sphinx bug specific to RT indices.
Sounds to me like some manual recover code could be written in the event of such a failure, a fallback should Sphinx fail.
Also sounds like RT indices are just plain bad period :D