You can do this in a couple ways,
However we do not have a single command line right now to disable the updater. It requires user action, see below. You could automate using script if you modify the ‘ini’ file below (option 2) using command line.
To disable Auto-Update check:
1) Using command line to prompt user with UI From the computer where the program is installed, open the command prompt and run this command: "C:\Program Files (x86)\QIPoint\SharePoint Essentials Toolkit\Check for Updates.exe /configure [HWND]" The user will be prompted to configure the update settings
2) Manually by config file: There is a config file that you can modify to change the 'check frequency' to let's say 1000000 days. By default, the location of this config file is below: "C:\Program Files (x86)\QIPoint\SharePoint Essentials Toolkit\Check for Updates.ini"