Despite the <span> tags overlapping my <ruby> tags, I got a basic <ruby> tag filter working. See attached ZIP file. This filter was tested only on Moodle 2.4.4, and there is no error checking, so use at your own risk.
Usage: [rb]Base Text[/rb][rt]Ruby Text[/rt]
The filter replaces [rb] and [rt] tags with <rb> and <rt> tags, and adds the enclosing <ruby> tag and <rp> tags.
If the Moodle community thinks this is useful, then let me know, and I will formally submit it.