Not an issue so much as running something 24x7 as root, but rather ability to manage accounts and access centrally. In other words I dont want have go to say 10 or 20 machines and change each password for given account, but rather do so centrally. Or have ability for example to add apache user account to a given group, have change made across all servers at once.

I can tell you that NetIQ is not solution for us, simple matter of budget. So can I assume if we changed authentication from Samba to anything else, be same?