Yeah, good point. If nothing else you reset the clock to zero, and that buys you an awful lot of time even under the worst case scenario.
"instead of a relativistic projectile, they sent a starship,"
A starship is a relativistic projectile that bothers to slow down. If you're going to smash a planet that acts up, you might as well just cut to the chase. All even-remotely-physically-plausible forms of interstellar travel are also intrinsically planet-busters, including the various exotic FTL drives that hover on the edge of plausibility.