I don't believe they would've been allowed to do that without evidence that KA had CA's passport in her possession. In the press conference, the US Marshal said that they figured out whose passport she was traveling under after conducting a physical search of that person and discovering their passport was missing. My guess is that they weren't able to search flight records for that individuals name until after the search.
Access to third party records (such as airline tickets) almost always have to be obtained via court order or subpoena, so my best guess is that the USMS weren't able to actually see if the passport had been used until they conducted the physical search and discovered it was missing, at which point they likely obtained a court order from a judge to search for that person's name in flight manifests.
A new set of Criminal Justice Standards on Law Enforcement Access to Third Party Records approved by the ABA House of Delegates in February 2012 appears along with commentary in a publication entitled: ABA Standards for Criminal Justice: Law Enforcement Access to Third Party Records, 3d ed. © 2013.
www.americanbar.org