There are add-ons for Jira which allow Single Sign on, such as https://marketplace.atlassian.com/apps/1212130/saml-single-sign-on-sso-jira-saml-sso
As for deleting users, if your Jira instance is configured to authenticate via Active Directory or LDAP then yes you can have users deactivated in Jira when they are dactivated in the directory.
You can activate SSO within some Atlassian products.
Depending on your host type, see the options for SSO implementation on this page.
By default, access to Atlassian products is managed separately via the Admin Console so a user leaving the company would need to be deactivated separately if no SSO is implemented.
Single Sign-on allows you to log in to the Atlassian Application from your IAM (Identity Provider) application.
On the Atlassian marketplace, there are third-party SSO add-ons that provide SSO as well as user provisioning functionality, but de-provisioning is not supported here as deactivated users will not be able to SSO into Atlassian application because of that application will not be able to deactivate the user.
Your use-case can be achieve using user provisioning (through API or SCIM protocol depends what your IAM application supports)
I work for the miniOrange one of the top Atlassian Marketplace vendors. We have the SSO plugins for all the Atlassian applications and we have provided a customized version of the SSO plugin with this kind of functionality to some of our users.
Feel free to reach out to miniOrange support if you have any other questions on this.
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