EDIT: I committed some code to master that adds a --disable-save option. This turns off the automatic saves every 12 hours. Manual saves and saving on exit still work.
If you pull and build you will get it, or wait for the next release.
Another way to limit/change autosave timing is to edit this line prior to compiling
https://github.com/aeonix/aeon/blob/master/src/cryptonote_core/cryptonote_core.h#L159
epee::math_helper::once_a_time_seconds<60*60*12, false> m_store_blockchain_interval;
Change the 12 to something like 240 before performing "make" this way it saves only every 10 days