So, SmarterMail installs the packages it needs, by default, so all is working after an installation. If a particular package is unwanted -- like the gss-ntlmssp package -- you can uninstall it, then make any changes to SmarterMail. For example, changing settings not advertise NTLM. Just realize that the installer would install NTLM again on the next install / upgrade. So, you'd probably want to make a script to remove it after you perform any upgrades.
In addition, SmarterMail is installed as root, by default. If you want to run SmarterMail as a user, we'll be creating a KB that will have commands to further secure your system.
We have prioritized bringing an enterprise Windows experience to Linux with an easy install process that gets customers up and running within minutes. If customers want to further secure their systems and customize how SmarterMail is operating, that will be possible. We'll be highlighting these types of changes and releasing KBs throughout the BETA process.