The statement that electric field lines do not intersect, since in this case, one would not have a unique direction of electric field, is absolutely correct. The purpose of this electric field line formulation is to indicate the direction of the net electric field at that point in space.
The way out of your confusion is: Imagine any point in space which is exposed to electric field due to two independent sources. One could always construct a resultant as vector sum of the two. In this case, the electric field lines would correspond to this unique electric field strength, not as an intersection of the electric lines of force due to the two sources.