The javascript code is not printed in field's description on the created form of issue. (only when the form is in overlay).

To reproduce :
1°) Set in description of custom field (directly or by field configuration) :
<script type="text/javascript">alert('OK');</script>
2°) Click on create issue, an overlay appears
3°) We inspect the description of custom field and the javascript code is missing.

Moreover, when the create form appears in page (not in overlay), the javascript code is printed.

In your documentation, it should work : https://confluence.atlassian.com/display/JIRA/Fields+Allowing+Custom+HTML+or+JavaScript