This could just come down to a difference of opinion on the nature of divine spells, the functions of clerics and the meaning of excommunication, in which case you're right in your game and I'm right in mine. But I'll try and explain myself a bit further.
Clerics derive their spells from their god. Divine magic really is divine, not mortal, in that regard. Mortals may cast it, but if the casting were flagrantly contradicting the will of their god, they couldn't do it. This goes double for certain spells that imply a much more direct involvement of the deity -- the cleric is really just asking, rather than casting. Atonement is one of these. Excommunication would be another. Casting a spell to cut off a person for their sins, implies that the deity wants that person cut off for their sins. (Excommunication was used as a political tool, but a political excommunication in D&D would not be a divine spell. Excommunication by magic implies the deity's assent, which is much closer to its intended meaning: you are cut off from divine care and protection.)
Actually, I think I see the sort of rationale you might possibly be using -- the sort of setting where such an excommunication would fit. If we have something more like medieval Europe than traditional D&D, where there are several independent (competing) churches in the service of the same god, one church could excommunicate a cleric without that cleric actually being cut off from the deity. But this implies that the deity is not very involved in what is done with the divine power it grants to clerics. I don't think this is compatible with standard D&D, where clerics get their spells because they are directly connected to their deity, and so churches are pretty much accurate servants of the divine will -- such a church couldn't use such a spell without the deity's permission. (I understand Eberron does have a looser cleric-god connection, where divine magic does not imply divine sanction.)