If you draw them in separate container svg elements, then the can be positioned using normal css.
So you should be able to position them with isotope. If you give the svg elements class names / ids that are expected (the ones you set in the isotope config) by isotope.
D3 can also be used to generate divs not just svg. So if you're in need of simple shaps such as rectangles you might get away with just generating divs.
Note: This is a very old answer now, It appears that Isotope explicitly excludes svg (thanks Geraldo), I'd recommend using D3js for layout in full or html elements (for isotope) in this case.