She prayed for mercy.

Literal

She [topic-は] mercy [object-を] wished-for.

願う ('to wish, hope, pray for') is everyday Japanese, used for everything from お願いします ('please, I request') to 平和を願う ('pray for peace'). The phrase 慈悲を願う is solemn but unmarked — closer to 'pray for mercy' than 'beg for mercy.' The verb 願う shares its kanji 願 with the more intense 懇願 ('earnest entreaty'); they're cousins on a register cline, with 願う sitting in the everyday middle and 懇願 reserved for the most formal pleas.