You can prevent users from being able to disable it once it has been deployed and enabled in settings from ePO.
Policy Catalog > SiteAdvisor Enterprise Plus 3.5.0 > Enable/Disable > My Default (or whatever you have called it)
In the third option - SiteAdvisor menu option: if you deselect 'Enable' users will be prevented from disabling the add in.
To the other part of your question though, I would also like to have SAE be automatically enabled when deploying it without any IE or Chrome popup or notification to enable or not.
You can´t prevent it at all from being disabled in Chrome.
As per McAfee manual you can run a query against the systems having the SAE feature enabled or not to get an overview of who turned it off.
You can follow steps in KB77685 to keep users from disabling SAE in Chrome.
I was really glad to find that article. Many of my users were not enabling the extension no matter how many times I asked them to, now they have no choice