The warning issued by mysqltuner.py is actually relevant even if your cache has no risk of being swapped.
It is well-explained in the following:
http://blogs.oracle.com/dlutz/entry/mysql_query_cache_sizing
Basically MySQL spends more time grooming the cache the bigger the cache is and since the cache is very volatile under even moderate write loads (queries gets cleared often), putting it too large will have an adverse effect on your application performance. Tweak the query_cache_size and query_cache_limit for your application, try finding a breaking point where you have most hits per insert, a low number of lowmem_prunes and keep a close eye on your database servers load while doing so too.