In secondary groups, user will choose the one or which ones (depending on your settings) he wants to be.
No, this plugin do not force the user; it gives the user the option to choose, as stated in the file description. If you want them to be in a specific secondary group, then select only this group in the plugin settings.
Then give permission to them to uncheck the group in the Account Settings:
With this permission, they will see in their Account Settings:
Then it's enough to uncheck the group and save.