I got this exact same problem, except Command told me to depart after the last Vasudan freigter wing warped out. I personally watched then all warp out too, I even destroyed the last remaining fighters before jumping, I get mission succeeded and failed debriefengs, and FS wouldn't let me accept.
*Cries* And it was so fun up till then. (Yay! Nav buoy game!)
Good ending too, makes you wonder what's going to happen next. All-in-all, two thumbs up.
Glad you all are enjoying it so far.

I'm currently half-way finished FREDing Episode 2, and after I'm done with the second half and after playtesting, it should be ready to go.
Ferret, Mefustae, and everyone else who's having issues with Mission 8: I'm still trying to work out a solution to getting that freighter bug fixed, but without any of the post-3.5.5 (my FRED build) features to aid me, I seem to be rather limited in trying to find a solution to this. However, I promise that I will find an answer, even if I have to get a little creative in getting there.
Also, SCP team: Thanks for working out the technical bugs. As a person with little technical expertise of the game, it's a huge help.