That's just the way it works.
If you have evidence that someone committed murder, do you let him go? Why not? Hundreds of other people have gotten away with murder free and clear.. how is THAT fair?
It isn't. But the answer isn't to let everyone do whatever the fuck they want. The answer is to punish those you can catch, and hope the possibility of being caught is enough of a deterrent for the rest.
And they'll never roll back 12 games a season. Losing 12 games per team is 180 games a year for MLB. Average 20,000 attendance per game, that's over 1.5 million tickets not sold. No way would anyone be willing to lose that revenue.