I completely understand your frustration. I've heard similar stories from other GoDaddy customers.
Unfortunately we're up against a mysql limitation. There's not much we can do about that. $200 plus for them to change that is insane!
My suggestion is to contact a few other hosts to see if they can offer what you need. You might consider a VPS solution. It's a little more expensive than shared hosting however much less than GoDaddys quote.
Both Stefan and I have used Liquid Web for years. I would contact them about your needs and get a quote. They are great to work with and have awesome support.
I hope this helps.