Kiera made her choice between the Alecs on Continuum Season 3 Episode 6, but it was less of a choice than a move of desperation.
Catherine told her having the two actively participating in the timeline was no longer going to work and she had to make a choice. Although it has seemed through the first five episodes at different times that one or another was an obvious choice, Kiera still bristled that killing one was the only choice.
A lot of what's going on in Kiera's head is a bit of a mess, and it's as if she was going to see the great and powerful OZ only to find a tiny man with a very loud microphone behind the curtain. The further she pulls the curtain away from what was her future, the uglier it becomes.