Currently there's now way of doing that out of the box! As long as a plugin package from WordPress.org contains your desired language file than it will be overridden on automatic plugin updates!
Only, if a plugin supports alternate folders for hosting the translation files, for example in "/wp-content/languages/" (or in a subfolder named like the plugin there...), then you're update secure.
You can only do manual updates or just re-upload translations or beg the plugin's author to integrate alternate translations locations.
Maybe the whole process changes in the future as WordPress might go towards "language packs" -- but no one of us knows yet how this will work in detail. Maybe, it will also be changed that plugin languages will be blocked from updates except for the admin of the site has this allowed or something like that. This option would be one of my faves :)
This whole thing is definitely a field where WordPress could and REALLY SHOULD improve! Internationalization seems not on the focus of too much core devs...
Hope this helps a bit, Dave :)