The thing is, the cruise rule exists to prevent shield running and help prevent capitals from... E-killing I think.
A fighter SHOULD be able to escape a capital by thrustering away. Sure, it counts as a retreat, but they still have their ship. A capital SHOULD NOT be allowed to cruise to catch upto him, as that would break the rules.
That's how I interpret it. If a capital really wants a kill, they better kill the fighter before he starts to flee...