Another option is to use extra_tags keyword arg to indicate that a message is safe. Eg
messages.error(request, 'Here is a <a href="https://stackoverflow.com/">link</a>', extra_tags="safe")
then use template logic to use the safe filter
{% for message in messages %}
<li class="{{ message.tags }}">
{% if 'safe' in message.tags %}{{ message|safe }}{% else %}{{ message }}{% endif %}
</li>
{% endfor %}