I'd still use IndieGogo, just not Paypal. The only alternative, however, is to use IndieGogo's own credit card processor, which charges 3%, but it might be worth it because funds are automatically ACH'd and you don't have to deal with Paypal... and the customer feedback is more direct.
But the big downside of this is that you don't get ANY of your money until the campaign is over (and up to 15 days after that), while with Paypal, you get your funds immediately (minus a 9% IndieGogo fee) if you elected for Flexible Funding. See http://support.indiegogo.com/entries/20578596 for more.
Given they only have two options: Credit Card from Indiegogo, which means no Paypal (yay), but also no money until the end (maybe boo) or Paypal (boo), but money right away (yay), it forces many folks to Paypal. They need to look at Stripe or Balanced or Braintree or something else.