Your problem would be solved just by activating the option “lock position/angle in the editor” on properties of your instance, but since version 5.0.122 it does not help anymore in this case, because the locked objects can be picked and you will always pick the object that is in front. I did a topic about that change explaining the difficulty that became working with many instances overlapping on the scene: About the dificulties with "new" Lock position/angle in the editor
I think the better solution is comeback with old “lock position/angle in the editor” (could not select the locked instance) and if it were really necessary to make the locked objects invisible do it as a second option.