Break the rules, don't get the money. Surprise!!?? After reading the entire email thread, I think Prezi comes out better off than the OP:
Actually we're continuously thinking on your case and struggling on the right move. On one hand, your finding was very useful for us, and we learnt a lesson from it. On the other hand, intra.prezi.com is out of scope, and by using the credentials to log in you violated the terms and conditions of our bounty program.
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In the past we turned down the bounty request of people finding issues in out-of-scope services. We had a lot internal discussions about your request: if we were about to pay, we couldn't justify our out-of-scope decisions for anyone else.