I always treated the "station atmosphere not yet decontaminated" message as a tongue-in-cheek remark amounting to "c'mon guys, give us a bit of time to work" with a kernel of truth. It stands to reason that clones -- particularly new ones -- would have a weaker immune system, at least from my limited understanding, given that they've not been exposed to the various pathogens and other nasties floating about. Best I can tell, though, it also seems reasonable to assume that there'd be the opportunity for a modified or cybernetically augmented immune system to try and sidestep this; both technologies are pretty damn advanced in New Eden. Another route would be 'old-school' immunomodulation drugs, I guess, shooting them up with immunostimulants.
Could clones left in storage for extended periods of time be sequentially exposed to the more common pathogens, perhaps, to generate an immune response before use, much like a series of vaccines? It's not a field I can ever claim to know well, but it seems reasonable.