Once you have the "#StartAtBoot: true", the service will always start upon boot - there is nothing you can do to stop this action when you set this option to "true".
However, if the service is not suppose to run upon boot, then you can simply add a check like this to immediately stop the service if it is not suppose to run on bootup:
Sub Service_Start (StartingIntent As Intent)
Dim RunOnBoot as boolean
'set value of runonboot to a stored preference value
RunOnBoot = [retrieve value from app preferences]
If RunOnBoot = False then
StopService("") 'stops current service
Else
'place your service code here
End if
End Sub