AFAIK, PiTiVi has no gui for batch conversions yet. Maybe what you can do in the meantime is to use some crazy gst-launch command fu, or use ffmpeg2theora, but it may be tricky; in the mpeg2-TS files I've seen, I had to clamp the framerates with something like this:
ffmpeg2theora --inputfps 30000:1001 -F 30000:1001 foobar.MTS
Also, if you're going to convert your stuff to ogg theora, make sure you have version 1.1 of libtheora and ffmpeg2theora 0.25; both are available in the "theora" Ubuntu PPA if you're using ubuntu. Theora 1.1 encodes files with much superior quality and they can still be read by 1.0.