Are non-GFCI outlets that are downstream of a GFCI outlet ground fault protected if they are fed from the GFCI outlet's load side?
Yes, that is the entire purpose of the load terminals of the GFCI.  You can imagine that the protection element of the GFCI extends both to its receptacles, and then just imagine the load pair as another "receptacle".  

As to the second part, yes, if you just connect the terminals together "before" the GFCI protection is in place, the GFCI will have no effect - remember, it can only sense problems on its own receptacles and its load terminals.