The transformation is not immediate
We see that it takes some time for the nanogenes to take effect:
CONSTANTINE: When that bomb dropped, there was just one victim.
DOCTOR: Dead?
CONSTANTINE: At first. His injuries were truly dreadful. By the
following morning, every doctor and nurse who had treated him, who had
touched him, had those exact same injuries. By the morning after that,
every patient in the same ward, the exact same injuries. Within a
week, the entire hospital. Physical injuries as plague. Can you
explain that? What would you say was the cause of death?
Doctor Who, “The Empty Child”
It took at least a few hours, possibly a whole night, for the injuries to manifest on the the nurses and doctors. The gas mask is probably the final stage of the transformation.
There’s a similar case in a later episode, involving nanogenes that convert non-Daleks to Daleks, which shows that nanogene changes may not take effect immediately:
DOCTOR: The air all around is full of micro-machines. Robots the size
of molecules. Nanogenes. Now that you’re unprotected, you’re being
re-written.
AMY: So, what happens? I get one of those things sticking out of my
head?
DOCTOR: Physical changes come later.
Doctor Who, “Asylum of the Daleks”
It’s not entirely clear why the nanogenes don’t act immediately on their victims, when they are able to reverse their changes and heal the Doctor’s hand in no time flat. However, a possible explanation is that the transformation can be resisted, as the case of the Dalek nanogenes shows us:
RORY: Fair point. Love this plan. What about Amy?
DOCTOR: Keep her remembering, keep her focused. That’ll hold back the
conversion.
Doctor Who, “Asylum of the Daleks”
It might seem odd that humans can mentally resist a physical, microscopic transformation, but this is readily explained. All human beings (perhaps all sentient creatures) possess some degree of latent psychic ability in Doctor Who.
CLEGG: Psychokinesis? Moving things by the power of the mind.
DOCTOR: A very rarely developed faculty in Homo sapiens. Professor?
Mister Clegg. Would you give us a demonstration?
CLEGG: Well, er.
DOCTOR: Please?
CLEGG: Oh, very well.
(Clegg concentrates on a tray over on a desk, with a plate and plastic
cup on it. Gently, it rises into the air and moves towards him.)
CLEGG: I can’t, I can’t keep it up.
BRIGADIER: You ought to use that in your act.
CLEGG: And lose my sanity? It would be a poor exchange.
DOCTOR: Mister Clegg, your powers may seem to be extraordinary, but I
assure you that they lie dormant in everyone. They’re perfectly
natural.
Doctor Who, “Planet of the Spiders”
While it does not usually rise to the level of the psychic power exhibited by the Doctor and the Master, for example, it seems quite plausible that it might be enough to allow people to resist being converted into a gas-mask zombie or Dalek by force of will (thus the need to mentally change someone into a Dalek before changing them physically). We see this sort of latent psychic power all the time in Doctor Who: say, in the third season of the revived series, where the mental power of humans (combined with a little help from the Archangel network) was enough to accomplish something pretty impressive.
Presumably people are resisting the nanogenes when they are trying to convert them into gas-mask zombies, but not when they’re trying to reverse that process.
