If you want to renew your passport in Thailand it is a risk that you are going to have to take.
The form doesn't go anywhere, it gets scanned at VfS Global to HMPO.
Is there a risk?
Yes, any time you put your 3 digit code ANYWHERE it is a risk.
Is dealing with this payment with HMPO via VfS a big risk ? No, hundreds of people do it every day.
In any event it is academic because there are no options, other than card, for making payment.
Send this to Virgin Money and ask them what you are supposed to do:-
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/190989/OS_Payment__Instruction_07.13.pdf