Individual 300x300 frames were probably still placed on a power-of-two surface the next size up by the GPU. So 60 x 512 x 512 images = about 62mb of memory. This is already high for an iPad 2.
Judging by what you say, C2 now exports 36 images on a 2048x2048 sprite sheet. That means all the images should fit on two spritesheets, taking about 32mb of memory total. So it ought to have saved a lot of memory. So are you absolutely sure this is the reason it won't start up?