Keeping spatial reference using arcpy.RasterToNumPyArray?

Check out the Describe method.

Something like the following should work.

#Using arcpy.env
import arcpy
import numpy

inRaster='C:/workspace/test1.tif'
outRaster='C:/workspace/test2.tif'

dsc=arcpy.Describe(inRaster)
arcpy.env.extent=dsc.Extent
arcpy.env.outputCoordinateSystem=dsc.SpatialReference
arcpy.env.cellSize=dsc.meanCellWidth

myArray = arcpy.RasterToNumPyArray(r)
myArraySum = myArray.sum(1)
myArraySum.shape = (myArray.shape[0],1)
myArrayPerc = (myArray * 1.0)/ myArraySum

newRaster = arcpy.NumPyArrayToRaster(myArrayPerc)
newRaster.save(outRaster)

OR

#Setting the raster properties directly
import arcpy
import numpy

inRaster='C:/workspace/test1.tif'
outRaster='C:/workspace/test2.tif'

dsc=arcpy.Describe(inRaster)
sr=dsc.SpatialReference
ext=dsc.Extent
ll=arcpy.Point(ext.XMin,ext.YMin)

myArray = arcpy.RasterToNumPyArray(inRaster)
myArraySum = myArray.sum(1)
myArraySum.shape = (myArray.shape[0],1)
myArrayPerc = (myArray * 1.0)/ myArraySum

newRaster = arcpy.NumPyArrayToRaster(myArrayPerc,ll,dsc.meanCellWidth,dsc.meanCellHeight)
arcpy.DefineProjection_management(newRaster, sr)

newRaster.save(outRaster)

EDIT: The The arcpy.NumPyArrayToRaster method takes a value_to_nodata parameter. Use it like so:

try:
    noDataValue=dsc.noDataValue
    arcpy.NumPyArrayToRaster(myArrayPerc,ll,dsc.meanCellWidth,dsc.meanCellHeight,noDataValue)
except AttributeError: #no data is not defined
    arcpy.NumPyArrayToRaster(myArrayPerc,ll,dsc.meanCellWidth,dsc.meanCellHeight)