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

Usage:
chmod u+x sanitize.sh
cat <filename> | bash sanitize.sh > myhistory.tsv

Input: <filename>, the path to (a copy of) your bash history.
Output: myhistory.tsv, a version of your bash history with all personal information (non-commands and non-flags) replaced by its MD5 hash.

Dependencies:

• md5sum, the hash function we use. This comes pre-installed on Ubuntu, and installation instructions are here for Mac.

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