I can understand if the principle of the outrage is the time spent earning the gil that's gonna disappear becoming a total waste... But I'm not seeing any other reason for this to be a problem... Assuming you can't hide your extra gil in a retainer named Swiss Bank, it's not like you're gonna suddenly find yourself having to buy gear priced at 250,000,000 a piece, and you're stuck with a measly 99,999,999... You currently can't price a single item at over the gil cap, you're not going to be able to price items at over 99,999,999 with the new gil cap...
Even if you could price things at over the cap, how's that gonna work if no one can have that much on them at one time? If it's just a matter of you don't know what to do with yourself after your sales have netted you the gil cap, then I'd call the game won and move on >_>