My original thinking about the burning/exclusion of magic users from Imperial Armies pre: Magnus was that I get the impression that the Witch Hunters were given (or just took) free reign to burn ANY magic user prior the founding of the colleges. Since Magnus the Pious both magic (in the form of the Colleges) AND the Witch Hunters have been reigned in a bit under Imperial control. The Witch Hunters are officially servants of the Emperor (the temporal representative of Sigmar?) and they now have to live with the Colleges of Magic: some perhaps think they are a Sigmar-sanctioned necessary evil to use against Chaos, others perhaps miss the old 'burning times' and think all magic should be purged.
Thanks for the info about Magnus - I had always wondered where the religious significance of the Griffon for Sigmarites comes from.