I wonder, why http://en.wikipedia.org/wiki/Boeing_YAL-1 is not CO2 one?
Are the issues with air transparency at 10um? Or it's impossible to focus on large distances due to diffraction?
COIL is 1.3um compared to 10.6um for CO2 so to get the same diffraction limit your optical components and telescope have to be nearly 10x large diameter. You can also route 1.3um through optical fibre (although I don't know if this weapons system does this) more efficiently than 10.6um and it's close enough to optical wavelengths that you can do a lot of setup and alignment with visible light.
Regular CO2 lasers operate on continual output, you can Q-switch them but even then I don't think you get the very high pulse energy of a COIL.
I think the as the laser is used for an airplane weapon system, it has to have a good power vs. weight ratio. The used laser is directly fed by the chemical reactants while the CO2 laser would rather use electrical power, thus having the need for additional electrical generator systems.
So the chemical laser system may give a better power to weight ratio, like a combustion engine running on fuel outperforms a electric engine running on batteries in weight, even if the electric motor is small and lightweight.