Batman had fire on his side. It's like Luthor beating up Superman while standing next to kryptonite.
I always figured the point of skrull infiltration is that they would lose in a head-to-head fight, and therefore needed to rely on sneaky tactics. White Martians can just pound most resistance into dust.
The 'Hyperclan' bit in JLA:New World Order seemed to just be a plan to get rid of the League, who were just about the only ones that could beat them in a straight fight. Their plan after offing the big seven seemed to be just a full-out invasion combined with mind-controling the populace. Why be sneaky when you can mind-control the majority and kill the rest?