Well, the way we handle missiles (and WC did that too) is quite different to freespace escpecially. In real life one missile kills another plane, but you can also only carry a handful, so it takes a strategy to save the missiles for the right target. Same does WC Gameplay.
I think especially people used to the freespace system can become a little depressed when first playing wing commander, but it's just a matter of experience, and then you can dodge every missile quite easily. But for gameplay it's much more better than having a fighter with 64 missiles and the "reload as often as you want" option. It's adds a complete new element into the fightsystem.