Converts rectangles to SMD pads in Eagle 6.x libraries. Since this is essentially a quick hack, you should isolate the package you are working with into a new library and copy the resultant pad data into the file manually.

rect2pad.py

import sys
from xml.dom import minidom

def main():
	print "Opening " + sys.argv[1]
	xmldoc = minidom.parse(sys.argv[1])
	
	rects = xmldoc.getElementsByTagName('rectangle') 
	print "Found " + str(len(rects)) + " rectangles"
	
	count = 0;
	for r in rects:
		dx = float(r.attributes['y2'].value) - float(r.attributes['y1'].value)
		dy = float(r.attributes['x2'].value) - float(r.attributes['x1'].value)
		x = (dy / 2) + float(r.attributes['x1'].value)
		y = (dx / 2) + float(r.attributes['y1'].value)
		print '<smd name="RP${0}" x="{1}" y="{2}" dx="{3}" dy="{4}" layer="16" rot="R90"/>'.format(count, x, y, dx, dy)
		count += 1
	
if __name__ == "__main__":
	if len(sys.argv) < 2:
		print "Usage: " + sys.argv[0] + " <library_name>"
		sys.exit(1)
	else:
		main()