kilele, support for existing java applets are not going to disappear overnight nor is the ability for users to run them if they so choose. Just don't upgrade to the plugin-less release and things will continue to run as they do today. The safest way to run applets (and Flash for that matter) is the same as it always has been. Only visit sites that you trust, be mindful if things don't look right or suspicious, and above all think before you click.
A lot of people, unfortunately, have developed an allergy to critical thinking so these safeguards won't work for them. As for long term, I imagine that applets will fade away and be replaced by HTML5 (or similar) equivalents.