There shouldn't be divine consequences for stealing from a temple. I like it how in DF right now, gods aren't tangible, like in real life (not trying to offend, but when did you last see an angel?).
I dropped acid two months ago. I saw angels, white mice and blue stars.
...but once you'd taken the acid, they went away, right?
Anyway, there is
one tangible god. You, in fortress mode. Arguably (currently at least) only has a limited range, and a limited range of powers (planting vague ideas for digging/building/etc into the local population's heads). To that end, I think stealing from a temple should at least give you a degree of persona-non-grata status from all the settlement's associated persons. But that's a bit close to the standard shop-lifting reaction, so perhaps it's a bit more wide-spread. Active hostility from priests (possibly some suspicion, in case you repeat, but initially and overtly more friendship from priests of non-aligned temples), gruffness from the local populace according to their alignment, and possibility of attack from local warriors/law-givers in a like way.
Further afield, might depend upon the connection to the site of the desecration (also lines of communication), tailing off or (as per the unaligned priesthood) even turning into a positive rep of kinds. Perhaps robbing some other town's temple and then
gifting the loot would be a good reputation-enhancer. Selling it (if possible) might be seen as little more than a mercenary action, of course.
With appropriate levels of sneakery[1], of course, the source temple might not be aware of your action (doesn't stop the god knowing, but might make it harder for them to justify the thoughts of violence in the local soldiery) and the destination town of your ill-gotten gains might not care too much about their origin. I could see two towns being played off against each other (with increasing risks, with increasing patrols over any remaining artefacts). Maybe knowledge of where the artefacts ended up could spawn further opportunities, from open war between towns (you might be asked to lead an assault, if not both assaults in each direction!) to a more friendly 'recovery' agreement where you're asked to act as courier (all the while with a big target on your butt... which is Ok only as long as you're the
only active outlaw in the area, but the news may bring others into the area) in order to arrange an amicable return, and possibly also transport reciprocal gifts of great (financial, not spiritual) value in thanks.
Shopkeepers Guilds and Mercantile Estates might have their own equivalents in the place of the existing shop-lifting incidents, various armed forces might have military pacts which allow trans-settlement (or civilisation?) warrants to be issued (or rewards for bad behaviour amongst the enemy!), and either further associations amongst the other professions or a general settlement/civ-based reaction alongside all the rest of the specific reactions.
[1] Traditional sneaking and the use of disguises that I recall being mentioned in the devlogs.