Paul,
If you need to leave SSH access enabled then you can limit it to certain IP addresses by doing
/sbin/e-smith/db configuration setprop sshd AllowHosts xxx.xxx.xxx.xxx
/sbin/e-smith/signal-event remoteaccess-update
You can add multiple IP's, just comma seperate the IP addresses.
You will still get the rkhunter message daily but you will know that SSH is secure and only accessable by IP's you choose.
The other way is as Stuntshell has already said. Disable SSH access in the server-manager and when you want to enable it, log into server-manager remotely and enable it.
I recently acquired a new customer who had his server (not SME) hacked by a hacker who installed a rootkit and an ebay phishing site. They got in by running a dictionary attack on SSH.
I trashed the server and installed SME

All SME servers I look after are now are limited to a couple of IP addresses for SSH access.
If I am out on the road and on an unknown IP, I have a server that I use that has full SSH access enabled and I SSH into the other servers from that one. I only have one server to check the SSH logs on and it can easily be trashed and rebuilt if needs be.
The third option is to use certificates. That way you can install the certificate on any machine and access SSH that way. There is a good How To for this. You will need to search for it
Jon