There is a filter called plugin_action_links that lets you do this.
function wpse253902_disable_plugin_deactivation ($actions, $plugin_file, $plugin_data, $context) {
if (array_key_exists ('deactivate', $actions)) unset( $actions['deactivate'] );
return $actions;
}
There is even a filter plugin_action_links_{plugin_name} that lets you control the links on individual plugins. If you dive into it, you will find out that you can also use this to define your own links.
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