I actually wonder why Sherlock is so sure of this and why the terrorists (or whoever they are) are so certain to kill Irene. BECAUSE the Holmes brothers felt sure of this, they let her go pretty much unconditionally, so it wasn't like Irene had to testify against someone or lead the British government to the cell, in exchange for leniency?
I know with these kinds of villains it's common for them to fall out and for one to kill the other for "failing," but why had Irene failed? What was to stop her from going right back to doing...her thing...once the Holmes brothers let her go?