There is no way in hell 97% of the population voted in favor with 80+% turnout; especially given that 30+% of the population is Tatar or Ukrainian. Based on leaked reports to the Kremlin the real turnout is estimated at a bit over 30%.
Regardless; the referendum was literally held at gunpoint after all Ukrainian news had been shut off and Russian television showed massive fascists uprising and murder in Kiev, which heavily scared the population and did make a large portion of the population believe they were being rescued.
Thus, even if the results were true, it still would not have been a valid referendum.
As for the protests, based on direct sources from real people the protests were organize by just that: real everyday people.
Once again though; the regime was not overthrown by the protesters, but by Yanukovich losing moral authority after ordering shooting of civilians.
If you want to argue the snipers were also a false flag operation then you'd indeed be well into conspiracy nut territory; but I can also point you to videos of Ukrainian snipers assembling if you want.
Global Research also doesn't have that good of a reputation. In [1] it explicitly mentions one of it's main reality warping effects comes from a heavy reliance on Russia Today material.