Her nanites ought to have been disabled by the field, why wasn't she affected? Is there an in-universe explanation that I missed?
They adapted the cloak to disable the replicator nanites. The cloak only alters things on the external surface of the puddle jumper normally, it doesn't extend a field inside the jumper itself. The field initially materialized around the ship and she stayed in the ship, so she wasn't exposed to it then. When she left the ship, the replicators had adapted to the field. So Weir's nanites could have also adapted to the field, as they were in communication with the replicators.
The cloak field might not propagate through the hull of the ship, and the generation is likely an external grid.