I agree with Bug and Christina- don't be cruel. Your son is FIVE- he doesn't get the larger spiritual or emotional implications of what is upsetting you. It sounds like you are taking this way too personally and letting it upset you, when this should be about your son and what is changing in his life to make him want to change his routine.
It sounds like with his dad going back to work and kindergarten starting, your son has a lot going on right now and is dealing with some of it by acting out. That is perfectly normal- don't take it personally! Remember, that kids act out with the people they love and trust the most, and that is almost always going to be mom!
Your job is just to keep things loving and stable for him. Ask yourself- what is he doing that is really so horrible? Changing his routine? Refusing to say prayers? You just keep to the same routine and say to him " Ok, if you don't want to sing a song tonight, let's read a story instead." Then read out loud to him and ask " Ok, do you want to say your prayers tonight?" If he says no, then you just say, " Well, how about if I say a little prayer anyway? I just like to tell God goodnight for you." Then say prayers just as you would if you were doing it together- teach by EXAMPLE, not through fear and guilt! Punishing him for something like that will just backfire on you and will not encourage him to pray when he is truly moved to do so.
He is just a child- you need to be the grownup here and understand that he is not a little kid robot who is always going to do things to your expectations. I know it can be hard, but you need to give him a little space to be upset and just love him and support him by acting the same way you always have and keeping things stable for him. Good luck- don't take this personally!