High morale seems to make it harder to flip -- it may not stop it entirely, but I've had far better luck rapidly flipping a system in the 50s or below than a morale-100.
Cultural resistance; yep, quite a bit comes from Evil, eventually. Early on it's hard to build 'tho.
Taking out an opponent's cultural starbases and, in particular, anything sitting on an influence resource would probably do the most to remove the pressure. A potential +68% global bonus to influence is quite powerful, and might well be worth a war to seize (or, more deviously, paying somebody else to go to war to remove the base).