Are you sure killing the bad guy is a win? Did it not go to the 2nd in Command?
Yes, you're correct that the 2nd In Command takes over if the Abductor is killed (assuming at least one Hostage is still in the Hostage Pool), and also that it's NOT a win if only this condition is met.
For it to be a win, ALL three of these conditions must be met:
- No hostages remaining in the Hostage Pool
- At least half of the hostages saved*
- The Abductor has been captured/eliminated
(Reference: Rulebook, page 13)
The OP wrote that he satisfied the last two conditions, but didn't mention whether or not he satisfied the first condition. I'm sure he simply neglected to mention the first condition, is all.
* Keep in mind that this includes any hostages added after the game begins, such as with the "I've Taken More Hostages" Terror Card.