touchy subject.... but if i may share my feelings as a mother of a 3 year old myself....i respect the feelings of others that you could just counter the effect of your JW ex-relatives by empowering your child with the ability to reason for himself but there is something more important to take into consideration....
your child is only 3... when he sees pictures in the "My Book of Bible Stories" of people on a rock as the flood waters are just about to swallow them up with faces of pure fear, or Lot's wife turned into a pillar of salt, or Jezebel getting thrown out a window for the dogs to eat her....(need I go on?)... this is not the shit you want your 3 year old to have to ponder over. These images are a brilliant strategy on the part of the society to begin their mind control through fear of our little ones.
Reason with your child all you want, but those are images and stories that a 3 year old will be affected by. As parents we don't let our kids watch blood and gutts movies, or see pictures of mutilated dead people etc. etc. Why would we allow pictures depicting a "loving" god killing people who didn't listen to him? No matter what you say to "undo" what he might see.... they are going to KEEP showing him the book, keep telling him stories, and keep trying to instill a fear in him.....
My vote is to put your foot down with the family.... this is YOUR child. It is YOUR responsibility to keep your little one free of all of the fear that those sick mind controlling cult members dish out to a child. I agree with all the others who said to get a restraining order and do whatever it is to make sure that they don't see your child again unless they stop. Give them the choice...if they don't listen, you gave them fair warning.
Remember something else here..... if they don't listen to you about leaving religion out of your child's life, they are disrespecting your right to raise your child.... and that sets a precedent for the rest of your child's life... do you want your child to eventually see that they have no respect for your role as the parent?? At first they don't listen to you about this....next it will be something else, and then something else... Put your foot down now and let them know that when you make a choice about the way your child will be raised, it's your choice to make and if they can't respect and abide by your rules...then there is no place for them in your child's life.
Good luck....
shannon