You’re making some pretty hefty assumptions. Blair becomes an evil admiral? And he alone is thereby responsible for Confed’s continued use of the fighters? Where is any of that to be found in the one endgame?
I’ll grant you that the mood of that endgame is brooding, but I don’t think that allows you to conclude Blair has become another Tolwyn. (For all we know, he might simply be dreading a scheduled dental appointment.) For that matter, we don’t know enough about the Black Lance fighters referred to to conclude they’re being flown by the same people or even used in the very same “ruthless” way.
I too would like to believe that Tolwyn’s comeuppance at the end of the game means that the Black Lance will be no more. But Tolwyn’s fall is prologue to both endgames, in which it appears that the only material difference has to do with Blair’s choice of a career. (And the conversation between Paladin and Blair in the one endgame where Paladin basically acknowledges that Blair can write his own ticket career-wise--and become a general, senator, or what-have-you--only complements the point.) Given that arguably trivial distinction between the endgames, we really aren’t in a very good position to draw any firm conclusions about the ultimate fate of the Black Lance (let alone the GE program or the Belisarius Group).