For some reasons BeautifulSouf does not convert entities with convertEntities=["xml","html"], use convertEntities=BeautifulSoup.ALL_ENTITIES instead.
{% extends "email/base_email.txt" %}{% load i18n %}{% block content %}{% if note %}{{ note }}
{% endif %}
{% blocktrans %}Click the following link to complete your registration and access the workspace:{% endblocktrans %}
{{ CONF.site_url }}{{ activate_url }}
{% endblock %}