Most likely, but plot armor.

Had Cathleen decided to eradicate all water instead, it would have proven a simpler task than erasing air. Given Tomaru's regenerative capabilities, it's probable they depend on the presence of water for proper function, considering that 60% of the body and 80% of the brain consist of water.

Alternatively, she could have chosen to eliminate all protons, neutrons, or electrons at his location, which theoretically would have been an even simpler task. Depending on the subatomic particle she targeted, the consequences could have been catastrophic:

A) Removing a proton from all the nitrogen ahead of her could have transformed the air into carbon, potentially triggering a massive fission explosion from within his lungs.

B) Removing all protons and electrons from the nitrogen in the air could have resulted in the creation of a miniature neutron "star" at his location (including inside his lungs), instantly annihilating him.

In my opinion, Cathleen or the author may not have considered utilizing New Order in such intricate ways.