1620s, "to pray against or for deliverance from," from Latin deprecatus, past participle of deprecari "to pray (something) away" (see deprecation). Meaning "to express disapproval" is from 1640s. Related: Deprecated, deprecating.
Said of a program or feature that is considered obsolescent and in the process of being phased out, usually in favour of a specified replacement. Deprecated features can, unfortunately, linger on for many years. This term appears with distressing frequency in standards documents when the committees writing the documents realise that large amounts of extant (and presumably happily working) code depend on the feature(s) that have passed out of favour.
See also dusty deck.