I assume you're referring to this Copy Merged extension? http://bit.ly/u1yN1
I'd be interested in hearing what's making it unstable for you. The default command handles locked layers just fine. If you have individually locked elements, you can run the Copy Merged - Locked Elements command to copy the merged state of the image.
I totally agree with you about the lack of a transform marquee feature. When I want to copy some pixels, what I usually do is draw a rectangle, which is easy to transform into the right size with my keyboard resize commands (http://bit.ly/CqSWA). Then I use the Copy Merged Into Selection command that's part of the Copy Merged extension. That flattens the image and crops it to the size of the rectangle, making it very easy to copy just the right part of an image.