Execution is unethical and barbaric, especially execution of an innocent person. Even if this means murderers are set free, just because they have murdered in the past does not mean that they will kill anyone else. However, there are many more choices then setting people free or murdering them - for example, prison.
While the argument that it's better to free 1,000 genuine murderers than to kill one innocent man may make sense on the surface, it needs to be looked at further. If 1,000 murderers are set free, then they are bound to murder far more than one more innocent person. While it's wrong for an innocent person to be executed, and everything should be done in that person's defense team's power to keep it from happening, it's really not a fair comparison to say it is worse than setting 1,000 people free who will go on to commit even more crimes.
No, it is not better that 1000 murderers be set free than one innocent man executed. If 1000 murderers were set free, many of them would commit other crimes, including murder. Then, more than one innocent person would be murdered, because they would become a victim of a freed murderer's later crime. False positives are a sad part of the criminal justice system, but anarchy is not the answer.