Can you not apply the pixellate effect to the whole layer, rather than the objects?
Nope, because then it tries to pixellate it as a whole layer, so with interpolation and pixel rounding off it just makes everything look like a mosaic censor.
I found a good solution actually! Thanks for the suggestion.
If anyone is interested, I upscale all my pixel art to 2x it's size when importing, resize it to half, and use Linear sampling.