Please run the script on a copy of your history and not the actual history file. This script only works on bash history. See usage instructions below. (code by Gaurav Manek)

sanitize.sh

#!/usr/bin/bash

while IFS='' read -r line || [[ -n "$line" ]]; do
	IFS=' =' read -r -a array <<< "$line"
	for index in "${!array[@]}"
	do
		if [ $index -eq 0 ] || [[ "${array[index]:0:1}" == "-"  ]]; then
			printf "%s\t" "${array[index]}	"
		else
			printf "%s\t" $(echo "${array[index]}" | md5sum | cut -c-32)
		fi
	done
	printf "\n"
done

For zsh, you can do the following:
cat <filename> | cut -d\; -f2 | ./sanitize.sh > myhistory.tsv