It seems that there’s a misunderstanding. It is possible to configure GanttProject so that the update window is not shown automatically, and this reply explains how: Need to disable the GanttProject 3.1.3100 update window - #4 by DmitryBarashev
It won’t prevent users from installing the updates manually if they wish. But they won’t see the update dialog by default.
Also, you can configure the update URL, so that GanttProject searched for updates on your own server (it is mentioned in this reply: Need to disable the GanttProject 3.1.3100 update window - #10 by DmitryBarashev)