Extracted baptisms for Charlton-on-Otmoor (including Murcott) can be found on the Family Search website (Batch No. C024372). Unfortunately, there's no sign of Thomas's baptism, although there are CLARKE baptisms in the late 1700s onwards.
What is your source for believing that Thomas may have been born/baptised in Charlton-on-Otmoor? Although it's where his and Frances's marriage took place, it's much more likely to have been the bride's place of birth/residence than the groom's.
Pennie