I understand where you're coming from, and fully agree that anytime someone goes to prison for something they didn't do, society is doubly worse off: once because the wrong person has been jailed, and once more because the real culprit has evaded justice.

That said, what you're describing is an issue with the practice of plea bargaining, not necessarily with giving less time for defendants pleading guilty. There are very compelling arguments that we should ban plea bargaining, as it's extremely one-sided, among other things. But while plea bargaining is partly enabled because the sentencing guidelines allow leniency for pleading guilty, I would argue we should keep the latter.

As a society, we should incentivize people to voluntarily come forward and atone for their crimes. If a murderer pleads guilty and divulges the location of the buried body, the victim's family can have a proper funeral service. But if that murderer instead flees, there's a chance that officers can make an arrest, but there's also a chance of successfully evading the law. Even if taken into custody, there's no requirement that a hardened murderer needs to reveal the burial location, and our laws prohibit beating that answer out of anyone.

A principle in law is that different criminal behavior should be punished proportionally. Ruthless killing versus accidental death. An accident versus indifference to human life. A clouded conscience versus a maligned intention toward the victim's family during a prolonged trial. This is what the sentencing guidelines seek to implement, moral hazards be darned.