Dauphin, we are not just bound by dogmatic definitions, but also be those decrees which instruct us to do something (or not do something)–that is, that are involved in the governing and pastoring of the flock since we are bound to follow our pastors as such.
Some medieval Councils were involved also in some civil law and such decrees should be treated as coming from that sphere(the one’s concerning the Jews you cited are an example of this).
Also, in regards to not accepting certain decrees to act, one cannot reject them merely on preference, but by conscience (in fact, this is the authentic use of conscience: choosing how to act or what act to avoid in a concrete situation given the truth that is known.)