He was chair of governors at the former church school and expects me not to apply for the post of deputy as he’s said he will be appointing someone with a faith background because the head is from the former community school. Can he do this?

I doubt it if the new school is a community school and not a “voluntary” school. It may be that some understanding was reached between the local authority and the diocese when the merger was agreed, but this should have been made explicit at the time. If the whole governing body does not support his view, I wonder whether he would be able to enforce it. Go ahead and apply and if you are the best candidate I hope you will be offered the job.