Give this script a geodatabase (Personal, File, or SDE connection) and it will remove the "Geoprocssing History" contents from the Metadata in every Feature Class inside the geodatabase.

remove_gp_history_geodatabase.py

#################################################################################
#
# Requirements: You'll need ArcGIS Desktop 10.1 or higher with Python 2.7 
#
# Give this script a geodatabase (Personal, File, or SDE connection) and it will
# remove the "Geoprocssing History" contents from the Metadata in every Feature
# Class inside the geodatabase.
#
# Before you attempt to use/run this script, make sure you have read the section
# near the top called "MODIFIABLE VARIABLES HERE". 
#
# Feel free to use, rewrite, and distribute as you wish.
#
#################################################################################

# Import arcpy module
import arcpy, os, string

## MODIFIABLE VARIABLES HERE
if __name__== "__main__":
    
    ## Use these variables if you are using this script in ArcToolBox.
    ## If you are running this script outside of ArcToolBox, then comment these two lines out, and read the next section.
    the_gdb = arcpy.GetParameterAsText(0)
    out_xml = arcpy.GetParameterAsText(1)
    
    ## Uncomment and modify to use these variables if you are running this script outside of ArcToolBox.
    #the_gdb = r"C:\LocalData\sandbox\New File Geodatabase.gdb"
    #out_xml = r"C:\LocalData\temp\remove_gp_history_xml"
    
    ## Make sure this variable value matches the path to your XSLT to remove geoprocessing history
    remove_gp_history_xslt = r"C:\Program Files (x86)\ArcGIS\Desktop10.5\Metadata\Stylesheets\gpTools\remove geoprocessing history.xslt"

## DEFINE FUNCTIONS
# Define dual console logging output function
def tellUser( message="\n" ):
    if message == "\n":
        print
    else:
        print message
    arcpy.AddMessage( message )

# Define the Dataset Feature Class iterator function (all FC's inside of Datasets)
def RemoveGpHistory_fd(the_gdb,remove_gp_history_xslt,out_xml):
    arcpy.ClearWorkspaceCache_management()
    arcpy.env.workspace = the_gdb
    for fd in arcpy.ListDatasets():
        arcpy.env.workspace = the_gdb + os.sep + fd
        for fc in arcpy.ListFeatureClasses():
            name_xml = out_xml + os.sep + str(fc) + ".xml"
            
            # Process: XSLT Transformation
            arcpy.XSLTransform_conversion(the_gdb + os.sep + fd + os.sep + fc, remove_gp_history_xslt, name_xml, "")
            tellUser("Completed xml coversion on FC \"{1}\" in dataset \"{0}\"".format(fd,fc))
            
            # Process: Metadata Importer
            arcpy.MetadataImporter_conversion(name_xml,the_gdb + os.sep + fd + os.sep + fc)
            tellUser("Imported XML on {0}".format(fc))
            tellUser("Geoprocessing History has been removed from {0}".format(fc))
            
            os.remove( name_xml )
   
# Define the Root Feature Class iterator function (all FC's not in a dataset)             
def RemoveGpHistory_fc(the_gdb,remove_gp_history_xslt,out_xml):
    arcpy.ClearWorkspaceCache_management()
    arcpy.env.workspace = the_gdb
    for fx in arcpy.ListFeatureClasses():
        name_xml = out_xml + os.sep + str(fx) + ".xml"
        
        # Process: XSLT Transformation
        arcpy.XSLTransform_conversion(the_gdb + os.sep + fx, remove_gp_history_xslt, name_xml, "")
        tellUser("Completed XML conversion on {0}".format(fx))
        
        # Process: Metadata Importer
        arcpy.MetadataImporter_conversion(name_xml,the_gdb + os.sep + fx)
        tellUser("Imported XML on {0}".format(fx))
        tellUser("Geoprocessing History has been removed from {0}".format(fx))
        
        os.remove( name_xml )

## EXECUTE FUNCTIONS
if __name__== "__main__":
    tellUser()
    tellUser( "Removing Geoprocessing History from Metadata for all Feature Classes in \"{0}\"".format(arcpy.Describe(the_gdb).name) + "...\n")
    
    # if the directory you input doesn't yet exist, then it will be created
    if not os.path.exists(out_xml):
        os.mkdir(out_xml)
    
    # execute Dataset Feature Class iterator
    RemoveGpHistory_fd(the_gdb,remove_gp_history_xslt,out_xml)
    
    tellUser()
    
    # execute Root Feature Class iterator
    RemoveGpHistory_fc(the_gdb,remove_gp_history_xslt,out_xml)
    
    tellUser()