It is really easy to mess up the command line when trying to process the xcode archive, and as a result delete the input file because the script treats it as the output file.
Example of bad command:
extract_xcode.py input_file.xip | cpio -d -i
This change prevents loss of gigabytes of data by simply refusing to overwrite the output file. The user can manually delete it before running the command, if overwriting is really he really intends to do.