Sure, that would be one way to hack around it. I'm wondering, specifically, if Stripe Checkout[1] will ever gain Apple Pay support. Presumably it's up to Apple to expose the relevant API to javascript.
my only issue with this has to do with the occasional lapse in recognition of the touch ID. if it can't read your fingerprint several times, it asks for your password code. touch ID is of course not theft-proof, but initially it's a slightly greater obstacle than a simple numeric code.
[1]: https://stripe.com/checkout