You're dead-on with #3. We used Amazon Simplepay for a subscription service, then recently switched to direct credit cards via Chargify. Subscription rates doubled instantly.

I wrote up some of my thoughts here: http://peachshake.com/2010/06/15/saas-subscription-billing-o...

Summary: Find a way to get the raw credit card. Bypass Amazon, Paypal, Google, etc.