Bloom is a screen-space effect — trying to apply it per-object is going to be a lot of trouble, particularly with a threshold of 0. Instead of two passes with different strengths, consider making these materials (much) brighter …
material1.color.setRGB( 1000, 0, 0 );
material2.color.setRGB( 0, 500, 0 );
… then use a single bloom pass and set the threshold to something larger than one. The goal here is to choose color intensities and a threshold high enough that non-emissive objects (even if they are white) do not exceed the threshold under normal lighting.