Do you really think the defendant committed that crime?
Literal
Defendant [subject-が] truly that crime [object-を] committing [quotative-と] you [topic-は] think [question-か]?
~と思いますか asks for the listener's opinion. 犯している uses ~ている for a resulting state: 'is in the state of having committed.' 本当に adds emphasis: 'really, truly.'