test.html

<span id="e116142240">[javascript protected email address]</span>
<script type="text/javascript">
    var a="gqMjyw7lZCaKk6p0J3uAUYS1.dbIW2hXzDHmiVNotOPRe_Ev@c4Gs58+LBr-F9QTfxn";
    var b=a.split("").sort().join("");
    var c="F_-F6F_-FMe_";
    var d="";
    for(var e=0;e<c.length;e++)
    d+=b.charAt(a.indexOf(c.charAt(e)));
        document
            .getElementById("e116142240")
            .innerHTML="<a href=\"mailto:"+d+"\">"+d+"</a>";
</script>
<p><span id="e49237979">[javascript protected email address]</span>
<script type="text/javascript">
    var a="[email protected]_s+H0N5E3naUWvfcyJ7oqBDO";
    var b=a.split("").sort().join("");
    var c="J+yJ4J+yJ@s+";
    var d="";
    for(var e=0;e<c.length;e++)
    d+=b.charAt(a.indexOf(c.charAt(e)));
        document
            .getElementById("e49237979")
            .innerHTML="<a href=\\"mailto:"+d+"\\">"+d+"</a>";
</script></p>
<p><span id="e186227798">[javascript protected email address]</span></p>

<script type="text/javascript">
    var a="[email protected]+RzqLT_WyhKOZsGEY9pjB";
    var b=a.split("").sort().join("");
    var c="GCsGwGCsGM.C";
    var d="";
    for(var e=0;e<c.length;e++)
    d+=b.charAt(a.indexOf(c.charAt(e)));
        document
            .getElementById("e186227798")
            .innerHTML="<a href=\"mailto:"+d+"\">"+d+"</a>";
</script>

test.py

import markdown2
import markdown
import textwrap
import random

def protectfilter2(email):

    character_set = (u"+-.0123456789@ABCDEFGHIJKLMNOPQRST"
                     "UVWXYZ_abcdefghijklmnopqrstuvwxyz")

    # temp list, needed to shuffle
    _list = list(character_set)
    random.shuffle(_list)
    key = ''.join(_list)

    tag = 'e' + str(random.randrange(1, 999999999))
    cipher = ''.join([key[character_set.find(char)] for char in email])

    script = u'''\
    <span id="{tag}">[javascript protected email address]</span>
    <script type="text/javascript">
        var a="{key}";
        var b=a.split("").sort().join("");
        var c="{cipher}";
        var d="";
        for(var e=0;e<c.length;e++)
        d+=b.charAt(a.indexOf(c.charAt(e)));
            document
                .getElementById("{tag}")
                .innerHTML="<a href=\\"mailto:"+d+"\\">"+d+"</a>";
    </script>'''.format(tag=tag, key=key, cipher=cipher)

    return textwrap.dedent(script)

print protectfilter2('[email protected]')
print markdown.markdown(protectfilter2('[email protected]'))
print markdown2.markdown(protectfilter2('[email protected]'))