The marking of a thing as no longer preferred, before removing it. Deprecation is a warning given in advance so nothing breaks unannounced.
Latin deprecatio (a warding off by prayer, deprecation), from deprecari (to pray against, avert by entreaty), from de- (away) + precari (to pray, beg); the marking of a thing as no longer preferred, a warning given ahead of its removal.
The Latin root is a prayer said to ward something off, not a command to remove it — deprecation asks a thing to fall out of use, it does not force the fall. The removal, when it comes, was announced long before it arrived.