I agree w/Bruce. I'd see if you can get the Builder to treat the rafters first, but it should be left to dry for a day or 2, depending on the amount of mix that's applied. He may not have a day or 2 to wait so I'd get right to it.
AT worst, the mold shouldn't get any worst assuming that air and moisture aren't continually being drawn onto that surface. Over time, it should just die.
One thing - You mentioned that this is occurring on rafters. Just to be clear, rafters are what 'supports' the roof's sheathing. If they enclose the area below the rafters w/drywall, be SURE that you have a soffit and ridge vent system installed BEFORE the area is enclosed. Soffit Chutes or Raft-R-Mates or the like should be installed on the UNDERSIDE of the roof to keep insulation from coming in contact w/the underside of the sheathing. The underside needs to breath (hence, the need for vents and chutes.) Talk to your Builder about this.