The Tavern

It's nice of the game to warn me that taking off a *Contam artifact "could" put me under penance with Zin.

Would've been nicer if the game had warned me before putting it on, like it does for a gajillion other things!

The Wrath description led me to believe that as long as I !cancellation'ed off the mutagenic glow after unequip, I'd be fine with Zin.

There is some inconsistency here IMHO.
Undead/lichform characters cannot wield holy weapons at all, TSO characters can wield weapon of pain but cannot attack with it without getting penance, Chei characters can wear boots of running but every step costs piety, Zin characters can use *Contam items fine until they decide to take them off.
Why can't we just have all those gods work in one and the same way? Like "this known item is forbidden and you will be excommunicated instantly if you try to put it on" and "This item has just been identified and is forbidded by your god. Take it off as your next action or you will be excommunicated". "You are going to cast Magic Dart while wearing boots of running, that will make you abandon Chei immediately. Abandon Chei (y/N)"

I like these idiosyncracies, because they give some items/gods/species more character for lack of a better phrase, by adding an additional layer of differentiation.

I accept that it's not clean design, and likely difficult to justify on gameplay terms.

These specific interactions don't come up often enough to be a serious concern in any case.

It looks like a variant of the fact that you can wield a scroll without warning, and you will be warned if you try to attack with it. Gods could get a special warning in addition to the normal one, even without added keypresses (Are you sure that you want to equip that trident of draining? Its use could put you under penance!), maybe with god colour. It wouldn't help me because I mostly don't read text messages, but, at least, it would be there. You could also have a god-coloured flash when the message is displayed.

In my Zin game all necromancy-branded weapons were colored red, and I did get a warning if I tried to equip one.

Come to think of it, I wonder how the game handles distortion branded weapons under Zin. If you can equip them without Zin-related comment, but then get the same warning that unquipping it could put you under penance (due to the risk of mutagenic glow), then I think I'd have to cede my point about *Contam.

I had a game recently where I accumlated a large pile of bad mutations, so I switched to Zin, reached full piety, then cleared them all. Somehow, I'm not sure how.. I think it was hell giving me glowing effect, I managed to get bad mutations again. It was very frustrating worshipping Zin, being stuck with the bad mutation, and then accumulating some mutation potions (which could likely have removed it) but not being able to drink them without incurring wrath. It seemed very backwards that the god of anti-mutations was the reason I could not get rid of a bad mutation. Zin used to allow drinking potions of cure mutation. I think perhaps, the cure all mutations ability should be reusable, just cost a hefty amount of piety.

I think there was a proposal in the past, that Zin should cure mutations as a passive over time. A bit like gifts with other gods, only you lose a mutation each time you'd receive a gift. It would correct this problem.

I really liked this and I thought this was actively being added. Did I get that wrong?

https://github.com/crawl/crawl/commit/8f7e939df157

So it looks like it is being done.