Question: How much damage would a space probe cause if it can get about 4 lightyears away in 10 years and doesn't have any brakes when it arrives? Could it cause a global extinction event on the planet it was sent to? Do actual concept probes think about this?

Answer: 
**Not enough to cause a global extinction.**

I could plug things into equations, but I'm lazy. Plugging [relativistic kinetic energy of a 100kg mass traveling at 0.4c](http://www.wolframalpha.com/input/?i=relativistic+kinetic+energy+of+a+100kg+mass+traveling+at+0.4c) gives $8 \times 10^{17}$ Joules. The page on the impact that is hypothesized to kill the dinosaurs, [the Chicxulub impact](https://en.wikipedia.org/wiki/Chicxulub_crater#Impact_specifics), says that the energy released in this event was $4\times 10^{23}$ Joules. 

A quick google search shows that the juno probe is about $3000$kg, or about thirty times heavier than the mass I plugged in. This gives that your probe would release 0.00006 times the amount of energy as in the Chicxulub impact. This is a lot, but not in the grand scheme of things!
The space probe won't do any damage as it will be vaporized in the exosphere. When the probe enters the interplanetary medium at a distance of the order of 100 AU from the star, it will collide with ions at a density of the order of a 5 ions per $\text{cm}^3$. The collisions with protons happen at a speed of 0.4 c, therefore at an energy of the order of 100 MeV, so this is quite similar to being exposed to intense alpha radiation. The temperature of the heat shield will be raised to about 600 K. The heat shield may tolerate temperatures up to about 6000 K before it will vaporize. This temperature will be reached when the density is $10^4$ times larger, so 50,000 ions per $\text{cm}^3$. But at 1000 km altitude above Earth you'll typically already have $\sim 10^{6}$ atoms per $\text{cm}^3$.

So, as the probe approaches an Earth like planet, the temperature of its heat shield gradually rises due to the increasingly intense bombardment of the ions and atoms it scoops up. At 10,000 km the shield will be red hot, 0.02 seconds later when it is at 4000 km it will most likely have vaporized, exposing the interior to temperatures of the order of 6000 K. The entire probe then simply vaporizes completely before even reaching 1000 km distance.

The atoms the probe consist of will keep on moving into the atmosphere until they collide with atoms. Because of the disintegration, each atom is now "on its own" while in a solid only the atoms at the surface would suffer collisions. All the atoms will have collided with atoms from the upper atmosphere already at a height of a few hundred kilometers. In these high energy collisions, the atoms get ionized and will then experience the strong Lorentz force due to the Earth's magnetic field. These processes will cause the energy of the probe to get dispersed well above 100 km altitude.