The problem is you are making a HUGE leap in that assumption. Many prosecutors do not want to risk losing and/or investing resources and time into something where the risk could be significant. In many cases, they don't believe they are wrong, they just believe they don't have enough evidence to risk losing.
That is a giant difference from presenting everything and a jury of peers finding the person not guilty. In your situation, you are making assumptions. In the other, there is a 100% concrete decision which ends with the accused NO LONGER EVER having to worry about being charged for that exact crime again.
Edited to add: Another major component is, under the position you are arguing, there is still the possibility of the charges being reinstated, until the statute of limitiations(if there even is one in this case under that jurisdiction) runs out...There is NO WAY you would rather have your outcome over the other. But, the stress of the case and waiting for the verdict is something I am sure he is now happy to have avoided.