Since he couldn't prove his innocence, he had to leave his hometown.
Literal
Innocence [object-を] prove could-not [because-ので], he [topic-は] hometown [possessive-の] town [object-を] leave must-did.
無実 = 'innocence (in a legal sense).' 故郷 ('hometown, home village') has a slightly nostalgic or literary feel. 去る ('to leave, depart') takes を for the place left behind. A tragic narrative sentence.