That is a tough one.. I agree with Harty and Deb both though..
First, all we can offer on here is our own personal opinions. We all have our own histories, baggage, etc... which influences what we may offer as feedback.
That being said, this is your decision and you ARE the one who has to live it. Don't let anyone make you feel guilty as long as you are doing what you think is right and is best.
I will say this.. that no matter what she does - she is your stepmother and if you father truly loves her - she is not going anywhere and will always be part of your life. If it won't put a huge crimp in your ceremony; I would be the better person, rise above her pettiness/cruelty and let her come. Talk to your Mother and make sure that she knows that you are only inviting Evil Stepmom out of respect to your Father; that she is the Mother you want there and love.
If you truly can't stomach her being there; then I agree with Debs - just do a church ceremony with you and FI to nix the drama.
Like I said, that's just my opinion and everyone on here will support you no matter what you do.
Good Luck!