Hey, I have this pattern! It was the first one I bought four years ago when I started quilting, and I decided it was too hard for me and didn't make it. I may be brave enough to try it now.
BUT, I thought looking at my pattern would help answer your question, and it doesn't. I can just tell you what I would do, which is just what you suggested, square them all up the same size. However, rather than cut 1/4 inch off of two sides, have you considered cutting a bit off of each side instead. That would leave you with the basic shape that you were after. It would be more trouble though.
At any rate, you can just decide that your design won't quite match the one you started to make and go with it. You can call it "creative changes." I suspect it would still look good.
Pictures would help though...anyone wanting to google the pattern....assuming I really have the right one... it is Diamond Double designed by Daniela Stout.
Dina