I'm supposing he meant that the body damage was the only damage, and that the known cost to repair the body exceeded the market value.

But OP states that, body aside, the car's condition was suitable to deliver at least two more decades of driving time. Buying a different used Civic at market value would introduce an unknown, unbound cost of repairs to reach that goal. Unless you're a mechanic it's essentially gambling. Or* it's a new vehicle-- in which case it will cost vastly more than the cost of the body repairs.

I suppose I understand why the market is relevant-- if it were $1 then it would be worth the gamble. But given OP's goals and foreknowledge of the car's condition, I don't understand why market value would create a hard limit against paying for the repairs. That foreknowledge is worth at least a few hundred dollars, probably way more if you factor in time to find another car and risk of it being in ill-repair. Edit: (Not to mention the depth of knowledge since OP had been driving it for nearly a decade already!)

Edit: Plus the fact that OP would have run this car into the ground. So while market value still plays some role, resale value does not.