You have to fly really low (below 50ft Above Ground Level) to get close enough to the S-300 System to take it out.
Youtube Video: https://www.youtube.com/watch?v=tN3_Zy4Hdhw Souptrooper Difficulty
I made this to practice flying really low & taking out S-300 systems. You have to stay under 50ft AGL to get close enough to an S-300 System to drop a gliding bomb on it. Use the GBU-38's for that. Navigate to Wypt 1 before flying in. Wypts 4 & 5 are the S-300. After that you can take out the Weapons Factory at Wypt 3 & the A-50 AWACS at Wypt 6.
Don't play the Long version until you've beaten the Short one, because it's really frustrating to make it all of the way there and then get shot down. Souptrooper is the hardest difficulty. I covered the map in MANPADS too so it's easier to be shot down and in the Long Version you have to fly all the way into the middle of Iran from the UAE while flying low enough that you don't get shot down by S-300's, Buk's, Manpads, Hawks & Rapiers all over the map. Try to find a weak spot to sneak in and use the same way to get out, but manage your fuel carefully! You're not going to completetly take out the weapons factory on this difficulty with 1 JDAM, because you only have the smaller diameter gliding bombs due to the weight resistrictions of the mission so just damaging it is enough to consider it a success on this difficulty, but maybe try a delayed fuse on it. There's a chemical tank above the factory part I hit. I had it on instant in the youtube video so only a couple of the tanks exploded. The delayed fuse could go through the tank and into the factory possibly. You could also hit it with 2 of the GBU-38's and just hit the A-50 AWACS with a sidewinder if you want, but you don't have much fuel to waste. Once you get to about 7000 fuel, head back out and land on the Carrier.
