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If you're going to run a criminal hedge fund, make sure it's big

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If you are going to run a criminal operation that also happens to be a hedge fund, make sure you are a goliath fund with ties to all the most influential Wall Street firms.

That's one of the clear messages conveyed by the Justice Department's decision to agree to a "protective order" that will allow SAC Capital to continue trading while under a federal criminal indictment.

If SAC were an ordinary hedge fund, with just a few hundred million dollars under management, it would be out of business the moment it was under indictment. Most likely earlier, as Diamondback Capital and other firms have been forced out of business just by being the subject of investigations. Investor redemptions would drain away the assets, counter-parties would close down credit lines, employees would fill recruiters offices.

But it's going to be a while before the last person at SAC Capital has to shut off the lights on the way out the door. It may never happen. And a major reason for that is that SAC is so large that regulators and prosecutors worry that its sudden demise would disrupt markets. No doubt trusted investment banking executives have helped them reach this opinion, which probably had nothing whatsoever to do with the huge fees SAC pays to those investment banks.

(Read more: Wall Street's big SAC Capital problem)

This isn't wholly a disaster. It's a terrible shame that an indictment can ruin a firm even before a trial begins. The market seems to have little patience for the presumption of innocence. So it's almost laudable that SAC has not been done in by accusations the government hasn't proven.

Except that this isn't likely the result of anything except SAC's tremendous size and influence. Which means that once again our legal and financial system has found a way to reward being very, very large. It's another version of the Too Big To Fail problem that is still, it seems, very much with us.

—By CNBC's John Carney. Follow me on Twitter @Carney

Wall Street