This is how I would do it (it requires the Spatial Analyst extension which I think you have):
from arcpy.sa import *
arcpy.CheckOutExtension = "Spatial"
ndvi_raster = Raster("ndvivaluefrompixel")
grey_raster = Raster("grayscalepixelvalue")
output_raster = Con(ndvi_raster >= -0.000005 * grey_raster + 0.314367, 2, 1)
I think you should use set the extent of the output in the Environments of the Raster Calculator to match your larger raster (Raster 1).
(here, you should add your Raster2 extent, otherwise use other options like Union of inputs that might work as well)
Then do a Conditioal expression like (not tested):
This should output a ...