I am not a lawyer. I am not suggesting any course of action. Under the facts presented by the OP, I describe the following course of events as not violating Amazon's agreement. OP's client contracts with OP to produce an EPUB for client to sell on website. Client asks OP how would this ebook look on Amazon devices. OP runs Kindlegen on the EPUB and sends .mobi output to client. Client never uses Kindlegen and is not bound by the agreement between OP and Amazon. OP uses Kindlegen in a manner directly permitted by Amazon (to convert documents and preview them).
I'm not seeing the problem with Kindlegen licensing terms in this scenario.