If you are guilty a plea deal is a good deal. If you are completely innocent, and have some money to defend yourself, you have a moral obligation to fight the charges. (Note: I'm no expert on moral authority, it's just how I feel. Sorry)
EDIT: Why not make it a law that when you are found innocent then prosecutor's office should refund whatever it cost you to hire your lawyer?
The question, though, was whether a person in a criminal case would be reimbursed the cost of their defense by the government after being found not guilty.
Even worse is when the evidence is poor but they want to convict the guy anyway because he looks like a bad guy. "Even if he didn't do this, I know in my heart that he's guilty of other crimes."