The first. He wished, at the time, that it would soon be over.
The second would be appropriate if the back-story were different. John's last train was at 11.00; the show finished at 11.05. He says to Kate 'I wished that it'd been over sooner.' In this case note that the "it'd" expands to 'it had' and not 'it would'. To have an 'it'd' that expands to 'it would', the context would have to change again. John explains about his train, and Kate says 'It'd have been better if the show had ended sooner'.
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