packaging: setup: Remove keys on cleanup after upgrade

Remove engine_id_rsa, apache-ca.pem and apache.key.nopass on cleanup
after upgrade from 3.2.

Before this change, many other files were removed in such a case, but
not these ones.

Change-Id: I06a015fa56594997a17ae073b12b0fcab1c11be7
Signed-off-by: Yedidyah Bar David <didi@redhat.com>