The more you study Bach's work, the more you get the impression that he didn't really prefer one instrument over another. The man routinely took pieces that had been originally written for one instrument and reworked them for another. He made violin pieces work on the harpsichord, harpsichord pieces on the pipe organ, organ pieces on the violin, whatever. He really seems to have been more interested in the music itself than in the specific acoustic properties of any particular instrument.
Besides that, of all the works Bach wrote, the WTC specifically is probably the best suited for pianoforte. Virtually every other keyboard instrument available in Bach's time was tuned to a just intonation in almost every case, making them unsuitable to play this particular piece. A justly intoned harpsichord (or a set of justly intoned violins for that matter) would be fine for BWV1079 or 1080, but it clearly wouldn't work at all for WTC.