I'm not sure what your question is exactly, but I interpret it as this. Consider a finite set $A$ of points on the sphere $S^2$. We want it to have the property that for each two points $a$, $b\in A$, there is a rotation $R\in O(3)$ with $Ra=b$ and $R(A)=A$.
So each of these $R$ lies in the proper isometry group $G$ of $A$. This is a finite group (unless $|A|\le2$), and it acts transitively on $A$. So $|A|\le|G|$. The classification of finite subgroups of $O(3)$ is known. They are cyclic, dihedral, tetrahedral, octahedral and icosahedral.
I am sure the cyclic and dihedral groups will give you the configurations you want to avoid, with points on two lines.
The largest polyhedral group is icosahedral of order $60$. I suspect $60$ is your maximum number of points.