Actually Lima does have a subway, or rather a light rail system, in the south of the city. It's a small system which if I recall correctly connects Chorrillos (or maybe part of Surco?) with Villa El Salvador. It may be the "rump" of the system that Alan García's '80s gov't was building, the unfinished bits of which are still visible along Av. Aviación. Anyway, it's not an area where a lot of gringos go so I'm not surprised you haven't heard of it.

To the OP: The El Pueblo conference center is very secure, and a nice place, although food service is a bit dated. As noted above, the rest of Lima varies a lot, from safe and secure to downright dangerous. That said, as long as security is being planned appropriately, she'll be pretty safe, and I'm sure the visit will be a great experience for her. Who knows perhaps she'll even come home a Catholic?