Sorry, I missed your reply
The exact CSS for this depends on whether the Glossary is on the front page or within a course,
If the Glossary is on the front page, and if your theme has an option to add custom css, add this
.block_navigation .type_activity.depth_3
{ display: none; }
OR
go to Site Admin > Appearance > Additional HTML and add this to the "Within Head" box:
<style>
.block_navigation .type_activity.depth_3
{ display: none; }
</style>
If it’s within a course, it’s the same code but the depth_3 will be different. It may be depth_5 instead.
Warning: although this will remove the link to the Glossary, it will also remove the links to all activity modules in the Navigation block.
If this doesn’t work, post a link to the site and I can check the exact CSS code for you.