hmm, according to SH3 commander this isn't possible (at least not when you try it there)
I think this might be a hardcoded bug, I remember from way back playing stock that I tried this once and it ruined the save, crashes and whatnot
, i'm guessing you also let one of your other officers go? otherwise you'd have too many which could be the problem...
But I'm no guru on the subject, I'm sure one of the wise men like Jscones or one of the GWX guys can tell you,
hope you get it fixed...