Private companies have no obligations to honor freedom of speech. Google has every right to say that your content must get a passing grade from [insert black box]. If the black box happens to be designed to filter out copyright violations, it gets no special treatment from the law.
Having said that, the main reason for many of the oversensitive, automated bots, is that big companies like Google (who have user generated content), still need to be incredibly careful in the area of copyright to ensure that they are protected. I suspect that strengthening safe harbor would largely solve this problem.
I would also like a system where sites were highly incentivised to promote free speach on their platforms, but other than public pressure, I do not see how to do this.