As a simple mission it works well. The mission logic seemed to work as expected. Not bad for a first mission.
My main feedback would be that it is a pretty simply mission all around. I didn't really have to think strategically or consider how my enemies might react. It was very much a "shoot what you are told to shoot" mission. That's not inherently bad, I just prefer more complex missions. That also seems to be the way the community is going with mods like WiH. There is a thread I was just reading that was talking about capships acting like capships and not just deathboats. I try to take that logic all the way when I create a mission. How would pilots react? Transports? NTF command? Would they just send a few Medusas to destroy a transport they had left hostages on? Even more so, would they have left hostages on a boat that still had engine power at all?
I don't want to say your mission was bad. It was better than a lot of missions out there because it had premise, it had a twist, and I always knew what I had to do. Props for that! Now I want to encourage you to take it another level. Start asking those questions and think of FREDing more like being a military strategist. This will help you to take your obvious ability to FRED a solid mission to the next level.
Definitely keep working on FREDing.
EDIT: One other thing. Also try to consider how to make the player essential to the mission. In this mission, Alpha 1 is kind of a nobody. Stupid AI aside, my actions wouldn't have really altered the fate of the mission much. So also think about ways to make the player much more important.