I just learned pedophilia (aka child molesters) suffer from a mental disorder. Wouldn't that mean they would be excused from the criminal justice system with a plea of insanity?

No. Insanity for legal purposes is quite different than it a mental disorder according to clinical practice. And, in either case, having a mental disorder does not necessarily mean one is insane.

Finally, if one is determined to be criminally insane, the criminal justice system will still incarcerate the offender, albeit in a different institution and for "treatment" rather than for punishment.

No they do not meet the legal requirements for Insanity.

Ok... that's weird.