I'd be wary of using IPA because it may affect the glues used in the helmet, even if it doesn't attack the foam in any obvious way. And the manufacturer would probably advise against it (and many other disinfectants).
I doubt a hairnet would help, as forehead sweat is probably the biggest issue that will get complaints (I suspect people will react more to unpleasantness than any real risk of catching anything).
With regards to headlice, the CDC say
Spread by contact with clothing (such as hats, scarves, coats) or other personal items (such as combs, brushes, or towels) used by an infested person is uncommon.
but how uncommon is another matter (other authorities disagree, but anyway headlice die in a day or so off a person).
Ringworm (actually a fungal infection tinea capitis) may be more of a worry, but it's not common in adults to start with. Disinfectants can stop it spreading.
I don't know how maintenance of the bikes and helmets will be arranged, but I think passive or minimal-effort solutions are probably going to be best. Some ideas:
Just having plenty of helmets so they've got time to dry out thoroughly should help. It will cost more upfront but will extend the lives of the helmets so won't cost much more in the long run. Storing them where they'll dry quickly is a big step in stopping them smelling.
Cheap helmets with little or no absorbent padding over the foam part will be able to absorb less sweat, and shared helmets won't fit everyone very well anyway.
If you get better helmets with removable pads, someone can wash the pads -- but who? When? Where? (I have tried laundry bleach for destinking but find a good soak in homebrew sterilser most effective).
Regular users of these bikes (perhaps cyclists who for whatever reason don't bring their own bike to work) may be encouraged to use their own helmet -- perhaps a bulk-buy discount could be arranged. This would reduce the load on the shared helmets. I keep an old helmet under my desk, and would lend it with the bike I keep near work.