I don't know how much leeway "infected from the source" buys someone. Recall if you will that Gate was infected by a piece of scrap picked up long after the surrounding area had returned to normal. The Sigma Virus is supposed to die without a host; while a piece of Zero may have provided a "culture" of sorts for it to survive, I highly doubt such a method of infection is any more severe than the usual.
Likewise, coming to your senses at the brink of death is a fairly typical plot device, which Zero already used more than once, and in the X-series it's not even exclusive to the virus-infected. See Iris.
Signas was never referenced to have any special viral immunities. The Hunters in general are always working on new vaccines; naturally Signas would have access to any new developments.
Since the virus is difficult to analyze, getting an in-universe list of which enemies were and weren't infected is near impossible (part of the difficulty in diagnosing the "Maverick" condition, referenced to varying degrees in pretty much every X game since X5). There is absolutely nothing to say that any members of Repliforce (prior to X5, that is) were infected, much less any reason to believe that Colonel and General resisted an infection running rampant among their subordinates.
One intelligent Maverick that you're forgetting is Berkana; she was a member of Reploid research and development (MMXOCW, page 90). Boomer Kuwanger also had some pretty strong analytical skills; besides Sigma and Zero he was pretty much the only other Reploid who, prior to Xtreme2, made any effort to look deeper than the surface in gauging X's abilities.
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