PCLZIP_OPT_REPLACE_ NEWER
Might in 2.8. x version, the problem do not solve, the first step Zip file will be unzip in the temp folder and will be copied after prechecking to the module folder.
In the new 2.9.0. dev which will be available during the next days in the SVN, we are going other ways. It does not become immediately unzipping, we check the files contained in the Zip, examine info.php for valid entries. If OK, everything is extinguished within the module folder, and unzip afterwards immediately to the module folder. No detour more about temp.
Dietmar