I knew that Charlemagne had famously ordered the execution of any person that killed another on charges of witchcraft, and I believe that even a Pope condemned the belief. I assumed that the church changed its opinion in the new millennium, possibly due to Reformist tendencies, but was confused by the number of clashing decrees, penitentials, and synods that occurred around the same time which had strongly contrary arguments.
Condemnations of the belief in Witchcraft as unChristian, pagan, and heretical:
Council of Paderborn (785)
Saint Boniface (d. 754)
Saint Agobard (d. 840
Canon Episcopi (before the 11th century)
Condemnations of Witchcraft, which implicitly suggest its existence and power:
Synod of Tours (813)
Synod of Paris (829)
Regino, Abbot of Prum (d. 915)
How were these different writers, bishops, and kings able to reconcile these points? Was the belief in witchcraft another internal conflict for the early church as what Orthodoxy really meant?
There isn't a lot to reconcile here, but rather a reframing. At no point did any decree of Catholic Church or medieval Christian king accept the existence of witchcraft (maleficium). Most of these decrees state flat out that belief in maleficium was itself the work of the devil, a contamination of the brain, of dreams, seeking to steer the good Christian flock wrong. The actual act of maleficium was declared impossible: a delusion created by the devil, and to stand by that illusion as the real work of a human was a heresy^1 .
Here is Norma Cohn's translation of the relevant section of canon episcopi
...there are wicked women who, turning back to Satan and seduced by the illusions and phantoms of the demons, believe and openly avow that in the hours of the night they ride on certain animals, together with Diana, the goddess of the pagans, with a numberless multitude of women; and in the silence of the dead of night cross many great lands; and obey (Diana’s) orders as though she were their mistress, and on particular nights are summoned to her service. Would that they alone perished in their perfidy, without dragging so many others with them into the ruin of infidelity! For a numberless multitude of people, deceived by this false view, believe these things to be true and, turning away from the true faith and returning to the errors of the pagans, think that there exists some divine power other than the one God.
Prum, Burchard and many others picked this up and included it in their various editions of canon law pretty much as is; Gratian then included it into what became Church law in the 12th c. No synod that I know of conflicts with this.
This was the standard view of the Church through the middle ages and into the early modern period. For Catholicism, witches never existed, nor did witchcraft. For this reason the Church rejected the malleus maleficarum in the 15th century soon after it was written.
Heresy existed concretely, and any form of showing allegiance to the devil and more explicitly, his intercessors, the pagan idols, was punishable.
I've written extensively on aspects of this which can be found here.