im not smart enough to come up with a solution, that's what the HN community is for. The purpose of the piece was to shine light on a problem (lack of transparency in salaries at VC backed companies)
On that note, I'll throw out an idea - maybe the valuation of company stock is not accurate enough. If it were, the problem would be much easier:
big co salary = startup salary + #shares * (stock price - option strike price).
EDIT: diving one level deeper, perhaps a company needs two valuations: one for investors buying the stock (market driven), and an internal one that employees are likely to accept. The two numbers should be the same, but during bubbles there might need to be a gap between them.