Although they might appear to be dark priests at a glance, the THMs Guild actually is something far more mundane (but no less darker) than that - they're actually funeral directors, who developed their school of magic from the manipulation of aether they used in the preparation of the deceased for burial (even their Guildhall's name hints at this - an 'ossaury' is a container used for storing bones from multiple bodies). When you first join up as a THM, the Guild receptionist at the front desk clearly states their early history as such.

Of course this could easily be taken as being 'in service to Thal', the 'god of the dead' aspect of Nald'thal (and very much in keeping with Ul'dah's own reputation as being a place where 'money talks'), but considering they seem to be more interested in taking money from the estates of the deceased than actually praying, it's little wonder they have a bad reputation.