If they're separated and have no intention of reuiniting, validating a marriage that doesn't exist would be imprudent.
You're not getting it.
They were probably married for years, probably have kid(s), and they should be convinced to reunite. Just because there was a flaw in their original marriage vows doesn't mean they haven't been making use of the marriage debt, forming strong emotional/psychological bonds with each other, having children and forming 2-way bonds there, etc.
Hearing that a couple "separated and have no intention of reuniting" doesn't cause us to bat an eye nowadays -- heck, that eventually happens to ALMOST EVERYONE's first marriage, right? That's the one you make mistakes on when you're young. Usually your first marriage just lasts about 5-15 years. Then, when you're more mature, you get divorced and end up finding someone better for you, right?
That's the modern, pagan, godless world talking.
A couple separated with no intention of reuniting should be a rare tragedy -- and the Church should be thinking in those terms. They should react to divorce like a man from 1850, when divorce was scandalous and rare. A Catholic Church official should be a relic, a fossil, a dinosaur, a blast from the ancient past in this regard.
Now do you get it?