Why can't it just use MyISAM or InnoDB tables instead of MEMORY? That would slow it down, but it should still work. A lot of the reads will still be from memory anyway, although writes might be slower across the board.
It does use MyISAM for results to be shown on web pages. Use of MyISAM for temporary data makes the bot several times slower. Currently Golem needs about 1.5 hours to process ruwiki, about 6 hours for such dis-connected wiki as pt, 2 hours for de. All languages (106 with disambiguating templates tunned properly) take 3 days of processing for bot with interwiki spy off and 1 day without iwiki spy.
mashiah