It goes something like this A: did you do that? B: pray, no .....
And another example is "Just pray no"
Pray in this since is used in place of "please". It is from a Shakespearean usage, if I'm correct. 'I pray you' = 'I am asking you, please' Also, prithee = 'I pray thee'. Pray basically means to ask. To super-politely ask would be to ask, and add, if it pleases you.
In modern usage pray means ask a deity, and by extension hope strongly. "Pray, no" would mean "I really hope I didn't", and "Just pray no" would mean "Just hope/pray that the answer is no".