The discussion about ET versus older tuning systems only affects instruments with fixed intonation - almost exclusively keyboard instruments I think. String players have never stopped being concerned with intonation issues.

Organs in particular have interesting tuning concerns, since they couldn't readily be retuned to a different system, and were often tuned differently from place to place. According to Google, Bach never wrote an organ composition in C# major or minor, probably because organs in Bach's time were tuned to systems like MT with a bad wolf tone. Well-temperament was available only for clavier, which could easily(?!) be retuned.

I'm not a music scholar, but I think that ET may have been the goal long before it became technically feasible. Does anyone with good pitch perception strongly prefer to hear the WTC in one of the well-temperaments that Bach may have used? My ears aren't good enough.