If the rebate is to come through the PAYE system because, for example, a tax code has been changed then it should be paid on the next pay day. This is not a problem for a large business with lots of employees where £1200 can just be deducted off what they would otherwise pay to the Inland Revenue but for a small business it is possible that, to pay £1200, they would have to find money from somewhere other than the next PAYE payment.
Yes, it should be paid in one go but it would probably be helping the business if he accepted the idea of receiving the money in a couple of installments. He should still establish how many installments it will be though. In a good small business, doing small favours like this without grumbling often works out favourably in the long term.
If the rebate is to come from the tax office, he will have to wait until April, at the earliest, for the money.