Understanding mysqltuner Recomendations w/ Unused Catalogs
If you know that the MyISAM tables are not being actively queried, not only can you ignore recommendations for key_buffer_size, you could actually lower it.

What can you do with the extra RAM you just reclaimed? One or more of the following options:


OPTION 1) Add that number to innodb_buffer_pool_size
OPTION 2) Slightly increase max_connections
OPTION 3) Slightly increase by 1M (given to each DB Connection) one or more of the following

join_buffer_size
sort_buffer_size
read_buffer_size
read_rnd buffer_size



After restarting mysqld, rerun mysqltuner and evaluate the resulting recommendations. Taking key_buffer_size out of the equation is enough in your instance.