This Isotope plugin provides a modified version of the Masonry layout mode that is compatible with percentage-sized columns.

It was designed for Isotope v1, and I have no information regarding compatibility with v2.

Just include this script after the Isotope script, then use it as a layout mode:

$blocksContainer.isotope({
    layoutMode: 'sloppyMasonry',
	itemSelector: '.block-class'
});

Licensed under the MIT License.