Try editing tools/cocos2d-console/plugins/project_deploy.py to be this (around line 197)
#TODO detect if the application is installed before running this
# adb_uninstall = "%s uninstall %s" % (adb_path, self.package)
# self._run_cmd(adb_uninstall)
adb_install = "%s install -r \"%s\"" % (adb_path, apk_path)
self._run_cmd(adb_install)