Altar destruction has never existed in a stable version of Crawl. You must be thinking of another game.
Or you are thinking of something that did exist in a trunk-only branch: altar desecration (this is a form of destruction) in the name of Lugonu. It's been a while, and I cannot look it up right now, but I think reaverb did this. If you search the git log for "Lugonu" and or "desecration", you should find it. (Be sure to not look just on master.)
Sorry to be so imprecise.
Regarding your feature: I think as-is it'd be problematic. This feature is very hard to balance *and* to communicate to players (so they can make a reasonable estimate about the wisdom of this action).
Of course, I like altar destruction like the next man, so for the record, here is what I originally wanted: part of the backstory is that Lugonu is the evil or fallen (you could say banished) god and that's why she hates all the other gods (whereas tensions like Trog-Sif or Xom-Zin are more your family grudges that occur in any proper pantheon). So a worshipper would be able to desecrate altars and thereby gain piety while incurring wrath. This got coded but turned out to be unfun because there are so many altars.
I still think it is neat, and a welcome change for piety gain, so it'd be nice to give Lugonu what she needs. Obviously, altar desecration should then be more limited, and some ideas I had for that: (1) Lugonu asks you to desecrate an altar to one particular god she currently loathes most, (2) you can desecrate at most one altar per god (flavour: say that after doing it once, that altar will now intently watch the remaining altars), or (3) desecrating altars of the same gods incur wraths of others gods, too (they're helping each other).