One fact absent from the discussion is most states actually pay retailers to collect sales tax. For example, if a state/locality has a 6% sales tax the retailer collects the 6% but only sends 5.5% to the state. The "discount" is intended to cover the retailers cost of collecting the tax on behalf of the state. I haven't read the entire bill, and it seems to change frequently, but I wonder if this provision is included, a provision that would cover collection and forwarding costs for internet retailers.
In any case the MFA is an abuse of the Commerce Clause and has already been declared unconstitutional by the SCOTUS.