Several states have joined a consortium called the Streamlined Sales Tax Governing Board[1], which harmonized, standardized, and streamlined the sales tax policies between those states in order to support easier compliance across multiple states.
South Dakota's recent win at the Supreme Court[2] related to collecting sales tax from internet sales was due in large part to SD's very pragmatic and fair approach for out-of-state sellers (doesn't require you to know/care about local sales tax fluctuations and only want a base state-wide rate, exempts sellers with less than $100k of sales to the state, etc).
I'm with you in that I don't blame the state for wanting to collect taxes; stuff has to get paid for somehow, and states don't have the same infinite/unbounded pocketbook that the federal government has. But don't disregard what you said immediately after that - the difficulty with compliance is a huge hurdle. If the company could have made compliance a minor additional cost, they could bake that into their decision. Instead, it was an unbounded additional cost with unknown future repercussions and required heavy ongoing administrative work (it's another legal/accounting variable that adds potentially non-trivial overhead to all future legal and accounting work).
The streamlined sales tax stuff demonstrates the same type of collaboration that could be done to simplify remote employee administration, without having the full compliance baggage that comes with the same level of administrative overhead as if you had a full fledged office in the state. Doing so would make it far easier and less onerous to hire remote employees (or allow an on site employee to keep working for you if they move out of state). So it's still worth raising the issue to political figures, as it's very similar (if far smaller in magnitude) to the revenue loss they had by not making it easy to comply with sales tax stuff.
[1] http://www.streamlinedsalestax.org/
[2] http://thehill.com/policy/finance/393441-supreme-court-rules...