Well, 'X started faction Y' and 'X joined faction Y' are different types of messages which you can filter according to your message settings. My settings, long before EMF had interest factions, have always been to stick 'X joined faction Y' (but not started) into the low-priority messages tab or log. You already get alerts when factions are growing to potentially dangerous sizes, so I hardly see the need to be spammed about every faction join/leave, whether it be an interest faction or other faction.
Of course, there is no super-easy way to disable interest factions, and I can't comprehend the desire to do so based solely off poor message settings.