The Baal Hatrumos has a Tshuva about Paskening through trains we learn in Aggadah. He mentions how although the Gemara says that a Bris is on the eighth day so that the parents are happy (Mide’oraysa at that point there is D’mei Tahara), obviously the day doesn’t change when this is not the case.
Interestingly, we do find some examples of the Taamim being invoked. The Shallos Tshuvos Min Shamayim has an answer that women make the Brachah on Shofar and Lulav since the reason for these Mitzvos apply to them as well.
There are examples of Geonim Paskening by a Derabanan based on the original motivation of the Takanah. I recall this happening by Nesu’ei Ketanah.