Looking for some advice

The kx is worth more than the XR. Can she use a clutch?

you might be losing out value wise, but "value" is a very subjective term here.

How much "value" does a bike have when nobody will ride it, vs. the "value" of a bike that will get ridden a lot and is much easier to learn on? Also, how much "value" does a bike that requires frequent rebuilds have vs. a bike that is virtually indestructible?

personally, I'd make the trade if I were in a similar situation.

Don't make that trade!.If that kx80 is in good running condition then you can easily trade it for a 2000's xr80.