。
She was completely worn out from overwork.
Literal
She [topic-は] overwork [from-で] limp had-become.
くたくた is a 擬態語 (state mimetic) for being thoroughly worn out — completely drained, limp with exhaustion. Interestingly, the same word also describes vegetables boiled until they collapse into mushiness; the underlying image is the same loss of energy and structure. The construction くたくたになる ('become exhausted') uses に as the marker for the resulting state of a transformation, and ~ていた layers on the past progressive — 'had become and was in the state of being exhausted.' 過労 ('overwork') is a Sino-Japanese compound that has come to carry weight in modern Japan thanks to the well-known phenomenon of 過労死 ('death from overwork').