I'd take this back a step. What sort of juice are you using that have come out with a C. bot risk identified?
I'm certainly aware of concerns around vegetable juices due to the higher pH (IIRC there was a thing with carrot juice in the US?), but there are very few fruit juices where the pH would be expected to stray above 4.5, due to the inherent acidity of the fruit. You'll occasionally see some varieties of apple get into the low-mid 4s, and certain varieties of mango in some regions, but otherwise banana and coconut are the only things that readily spring to mind as potentially sitting in the low-acid / high pH area. If you're buying these as processed juices/purees there is a reasonable likelihood they been sterilised (rather than pasteurised) and/or acidified for exactly this reason.
Feasibility might depend on the specific "HACCP" system expected by your certification scheme and/or regulators (FDA may have different versions to the FSA here in the UK), but if all your juices are the naturally acidic types then you could instead call it a prerequisite that juice raw material specification pH is <4.6?
As you're in the US you might also be able to rely on the differentiation the FDA makes in the Juice HACCP guidance on high vs. low acid juices, as I believe C. bot is only mentioned for the latter.
I'd be cautious about the role of CO2 in this particular question. It will help with some pathogen types (but those are probably addressed by your pasteurisation anyway), but the presence of CO2 alone will likely be insufficient to address the C. bot risk, unless it is also effectively providing an acidification step and part of the function is pH reduction? That would strike me as a relatively inefficient way to achieve this though 
See e.g. this link on the effect of CO2 on proteolytic C. bot growth and toxin production - very little effect even at vastly higher levels than you'd ever reasonably be able to get into a drinks : https://www.ncbi.nlm...les/PMC2820955/
