Well done, both runways are closed. Runways cannot be destroyed but to quote Dimitris from the Forum:
Runways (and other air facilities) have what is called an "Effective runway/aircraft size", which takes into consideration both the runway's nominal aircraft size capacity and its current integrity status, to determine the true AC size class that it can handle.
Taking the pair of runways at Souda Bay as example (3500m):
Between 1% and 10% integrity only STOVL aircraft or helicopters can operate. (At this point you're literally looking at craters and broken chunks of concrete everywhere. Perhaps even the STOVL ability is optimistic, given that in such a condition the engine-FOD would be quite likely...)
The base is closed, the air defenses are down, and a follow up strike will likely turn the place into a smoking ruin.
Bravo! You now have the skills to tackle some pretty tricky targets. An SA-10 is not easy to defeat and could spell the end of a game for an inexperienced player. Now you know how to beat it, all you need is some decent terrain, some standoff weapons, some anti-radiation missiles, and a bit of luck. Simple!
You are ready to move on to the Multi-Domain Strike Planner tutorials or a beginner scenario like one of Uncle Marks Tutorials.