The short answer would be no. As Fhao said, payments via PayPal allow Poniverse to protect both the artist and customer from potential scams. In fact, before the escrow system was implemented, there were a handful of cases in which payments were taken without any art ever being produced. The current system, though not foolproof (because no system is), at least compensates artists and customers.
Integrating dA points would require additional management and tech workarounds which I suspect would be too complicated to implement. At present, PathfinderCS is the only staff member managing commissions on a day-to-day basis; more support would probably be required to track things like dA points. Moreover, Poniverse would lose its 15% cut from such sales, given that dA points cannot be liquidated, so far as I am aware.