[peterwwillis]

Well I suppose you're right, if you're using your bastion host as the TOTP operation service provider, but I wouldn't recommend that for a whole host of reasons - the main one being that the bastion host is always the first host exploited, so you shouldn't be running anything from there but a proxy.

You should be able to simply move the TOTP operation to an authentication server on a more secure network and have your web-application server query it with the user's token. The web app will get back the result of the operation and never expose the secret key to the bastion host.