Depends on the structure of your SVG files. Basically, you would need to select the circle object, find out where it is centered (if they are in different positions), then put a rectangle object into the same position. If the size of circle and rectangle is different, as in your png image, then you'd need to calculate the new position, too.

The choice of tools depends on your abilities. I'd probably not use the Inkscape command line for this, but an xml library in the language of my choice (in this case, python), or I'd create an extension that can be called from the command line.