In the book, the other Dons are all scrutinizing Vito as he speaks at the peace conference, trying to guage how healthy he is. It seems no one has seen him between the day he left the hospital and the day of the conference. For all Brazini knows, by killing Michael he might be decapitating the Corleone Family.

By targeting Michael (and if his role was discovered), Barzini could expect to earn whatever wrath Vito could muster - and if Vito was unhealthy he could even trigger a transfer of power to Clemenza or Tessio, who might be easier to deal with. By targeting Apollonia (and if his role was discovered), Barzini could expect to earn whatever wrath Vito could muster, plus vendetta from Michael, plus a loss of all support from other families, because he targeted a civilian family member. I don't see how that calculus works in favor of targeting Apollonia.