It's hardly that much of an ethical dilemma. If your company wants your miles, you give your miles. If not, then they are yours.
The more interesting point for me in the article is the idea of how to tax them as a perk. That has been discussed ad nauseam by our Internal Revenue Service (and prevented from becoming Code as well by our legislature). One of the tricky parts is the reporting mechanism and the taxation trigger mechanism. Is the act of flying a taxable event or is the use? If the former, do people get a tax credit for expiring miles? If the latter, do you tax on mileage value or ticket value? How do you separate personal miles for shopping or personal travel from the miles accumulated from business? As I said, the idea of the government attempting to track and tax my miles is quite a challenge.