Can I disable Google Software Update for a selected user account?
[repeating my comment as an answer to close the question]

When you update a setting using defaults, it generally only affects the current user." http://commandlinemac.blogspot.com/2008/12/defaults-setting-preferences-from.html

So I can just run 

defaults write com.google.Keystone.Agent checkInterval 0 

on each of the non-admin accounts where the pop-up is bothersome.