To further support Valorum's answer, the concept of the Force was based on a mash-up of religious concepts surrounding an idea of "balance", the most obvious of which ties to the concept of Yin and Yang:
The principles of the Force resonate with those of some real-world religions, including the Shinto religion of Japan, Buddhism, Taoism and certain Celtic druidic concepts. [...]the splitting of the Force into light side and dark sides echoes the concept of yin and yang in Eastern philosophy [...] Along with the concepts of yin and yang, the concept of a ubiquitous Force parallels the real-world concept of a "Tao" or "way," which is said to flow everywhere in the universe.
When we look at what the concept of Yin and Yang represent, we can see the relevance to how the Force is a sum of the whole, and the separation of the Jedi ("Light"), and the Sith ("Dark") moves away from what the balance should be (emphasis mine):
In Ancient Chinese philosophy, yin and yang (/jɪn/ and /jɑːŋ, jæŋ/; Chinese: 陰陽 yīnyáng pronounced [ín jǎŋ], lit. "dark-light", "negative-positive") is a concept of dualism, describing how obviously opposite or contrary forces may actually be complementary, interconnected, and interdependent in the natural world, and how they may give rise to each other as they interrelate to one another.
We can see this "yin and yang" symbolism represented in the image in Valorum's answer as well.
My original understanding was that the Jedi Temple being built on top of Sith caves and temples was to "Put a lid on it"; bury and smother it in a misguided attempt to bring balance to the Force, after the separation of the Jedi and the Sith, being that the Jedi believed that "balance" meant "snuff out the evil":
"The Jedi tried to cap the power of this shrine, but there's leakage. It's not just Sidious; it's the power of history, it's the residue of what's left of the dark side there."
Where the problem started with an "imbalance" of the Force was the separation of it, and the belief that the Dark side needed to be removed, or hidden must have been lost in translation, and buried in history.
So in summary, as Valorum stated, the original practices/studies of the Force embraced both "sides", as it believed in embracing all aspects, similar to the concept of Yin and Yang, but as the separation developed between the "light" and the "dark" sides of the Force, the desire to bury and hide any association with the "dark" side led to the Jedi cutting off, and hiding the associations the Jedi had with the "dark" side of the Force (i.e. the Sith Caves), which the original practitioners had built on (The Jedi Temple(s)).