If depends on why you're using the isolation transformer. At work we use an isolation transformer to power a piece of equipment with a very high earth leakage from an RCD protected supply. The whole point is to effectively remove the RCD protection so we do bond the secondary to earth and I've stuck a label on the transformer to warn people about this.
For most applications, as stated above, you shouldn't bond the secondary to earth as it defeates the purpose of an isolation transformer.