It was explained, even ingame if i remember correctly
Since the Force is a "living thing" that requires balance, it will act if a massive imbalance is happening.
The Rakata controlled the whole Galaxy and exclusively used the Dark Side, meaning there was a ridiculous imbalance happening. Since that imbalance couldn't be attacked by outside forces (like an opposing Faction, there was none) the Force had to take action itself.
And it indeed took action. By cutting of every single Rakatan from the Force.