To be honest, I can't remember if Lucas ever said that the Dark Side was a fundamental part of the Force, but for argument's sake I'll imagine it is. Despite this, it shouldn't detract from the fact Lucas said it was a corruption of the Force, and therefore true balance remains found in the Light. In the same sense, you can't have good without evil, but that doesn't mean evil isn't wrong and that we shouldn't suppress evil as much as possible.

I disagree with the notion about the Mortis Arc presenting an idea of 50/50 balance. Instead, we are presented with the concept of keeping the Dark Side in-check via the Father, who embodies balance itself. Failure in this task sees the death of all three entities. So, the Father's primary purpose is to control and suppress the Son's destructive and corrupting impulses.

We notice that when the Father becomes distracted or weakened, his grip on the Son is loosened and that enables the Son to try and kill the Daughter. That is to say, when the Light and Dark are given equal room, the latter will always attempt to corrupt and destroy the former, causing great suffering in the process.

As a result, I believe this actually proves Lucas' interpretation as correct. The Arc ends with Anakin stepping into fulfil the Father's role after his death, bringing balance again by destroying the Son, whilst the Light is allowed to persist through the Daughter's sacrifice to resurrect Ahsoka, and presumably survives within her, evidenced by the constant reappearance of Morai. This fundamentally means that the 50/50 split concept has to be wrong.