I would also point out that it was a research facility, and the research had only got as far as producing River (who would probably have been exceptional anyway). If subjects like River are 1:1M, and they could not succeed with her, then there are probably very few at quite her level of skill.
Even if there are 1 or 2, The Alliance probably has no real control over them either, and sending them out on such a mission would be highly risky.
So I think it is fair to say that River is the most talented of the experiments (not necessarily the most successful), meaning that there is no-one else they could risk sending.
I also think that part of the reason the Alliance wanted her back so much was that her story and what was done to her was a serious embarrassment to the government, not just because they wanted her talents back. Given the failure of their attempt to control River, letting other out into the general population would be even more risky.
The possibility that the Alliance could send their 2 most talented assassins against her, and that she could convince them to turn against the Alliance might have also been part of their thinking. I suspect that this would have been a real possibility.
We might have found out if Fox hadn't cancelled it, of course. That is a decision they will regret.