I think you're completely right about waiting for the forward thrusters to ramp down before firing the reverse ones. It's the kind of thing you would write down on paper when designing the system and not realize that it doesn't match up with the way the ship engines work. I'll explain why this behaviour is not necessary to maintain new flight model.
The problem (in my opinion, and I think nimrod's as well from his comment) comes about when you have multiple engines.
Of course some of this comes down to design decisions, and implementation considerations. But my guess is that it might feel (or at least look) more intuitive if the individual engines had ramp up/down times, instead of the overall acceleration being subject to a ramp up/down time.