Split the "Federal Sales Tax" into 3 pieces. One for the feds, one for the state where the goods are going and one for where they shipped from. All the merchant would do is report the dollar amount collected each month/quarter etc and what ever the percentages the law covers would be handled by the agency managing it. The smallest portion should be for the feds to run that agency. It would then be up to the states to figure out what to do with that money. It beats what most of the states get now which is nothing. States that don't have a sales tax could opt out. This would fix the problem of the sending state getting shafted and the feds having to run it for free.
Of course, the government being the way it is, this will get abused to no end.
One thing that bugs me about the deal that amazon got is that a small business would not get the same because they are just not big enough.