http://www.cnn.com/2003/TECH/space/09/19/galileo.crash/index.html
If I lived on Jupiter and some Earth missile came down in my city blowing stuff up, I'm pretty sure I'd want my government to shoot back, so Earth doesn't do it again.
Do you think this measly little probe will compare to those comets that hit the planet?
I think you can relax.
IIRC, Jupiter is not capable (or has a low chance of being capable) of life. However, Europa (one of its moons) has a high chance of life (frozen or non-frozen water was discovered on it), so NASA chose to crash the spaceship on the planet rather than the moon.
Well, maybe an alien space probe crashing on the surface would be just what life on Europa needed to evolve into the next stage?