Yeah, the gallery you are using wont work with Image Resizer because like you say, the full size image is taken from the a href.
Most JQuery and moo tools galleries don't use an a tag and would work, Power Gallery 2 actually uses image resizer to give you control of the image sizes, both thumbnail and large images.
in power gallery 2, you go to the gallery editor and set the size and cropping pattern to use for the thumbs and large images.