You can prevent WordPress users from being able to deactivate plugins by hiding the ‘Deactivation’ links.
Why
At first glance, it doesn’t make much sense to prevent users from disabling plugins within the WordPress admin. You certainly wouldn’t want to release a public plugin that prevents users from turning it off, especially since you have to deactivate a plugin before you can delete it. Let’s argue it out.
Me: “I think it would be appropriate to disable plugin deactivation when you have a plugin that is integral to the site and shouldn’t be disabled.”
You: “Yeah, but why not just use a must use plugin?!?”
Me: “If it is a custom plugin, absolutely. However, must use plugins don’t check for or show available updates.”
You: “Oh, so instead of having to manually update a must use plugin, if I disable deactivation for a public plugin then the user can’t disable it and can still see when updates are available.”
Me: “Right. You will also be able to update the plugin from the admin area, which you can’t do with a must use plugin.”
You: “It sounds like this would work well for publicly available plugins because they automatically check for updates. If I have a custom plugin that is set up to automatically check for updates, then this could be a great way to manage integral plugins across multiple client sites!”
Me: “Absolutely!”
How
The code below can be placed in a custom plugin. If you’ve wired the plugin for update checks, then you will get the benefits of easy updates without the downside of a client being able to disable or delete the plugin.
If you want to disable deactivation of a third-party plugin, then you will want to drop this code in a file in the mu-plugins directory and instead of using plugin_basename( __FILE__ ) you will want to hardcode the plugin basename.