The fact that "it's always been that way" is no refutation of the fact that "it's a problem" that you could lose money and yet still owe taxes as if you had gains because capital losses (hysteretically) saturate at $3000.
This is money, not "do whatever you want".
That said, it doesn't matter what is and is not "fair" when dealing with the IRS. Choice A is to do what they tell you to do. Choice B is to fight them in court.
This thread assumes you want to go with Choice A and that you want to limit your liability if something goes wrong. Like most risk-management techniques, it does decrease your returns.
(Tax lawyers might have some better advice. Perhaps you can mine into a blind trust, and pay income taxes in 5 years on the current value of the coins? Dunno, not a tax expert or a laywer. I would consult with one if I was mining a lot of Bitcoin.)
"Bitcoins earned through mining are considered compensation for providing resources to the Bitcoin network to compute hashes verifying transactions."
When viewed as compensation then the treatment seems consistent with NSOs or barter transactions.
They make allowances for things that are not liquid.
If I have accumulated $100,000 in capital losses over the prior ten years, I can wipe all of that out in one shot by producing a large enough capital gain in one year.
Capital losses saturate when applied to ordinary income.
i.e. would sales inside MTGox have counted towards this tax or isn't only with withdrawl/deposit into their ecosystem. I can imagine that if internal to MTGox interactions are treated this way then there are a lot of people who sustained a capital loss higher than that and had no option to withdrawl the money to pay taxes.