Morals aside, as a small nation, you simply don't piss off your big neighbour (except if your big neighbour is Germany, then the big neighbour will just say you're right
).
Also, the current russians living in Estonia can hardly be blamed for Stalin and I have experienced firsthand the troubles this strange estonian "quasi-citizenship" can cause.
The whole memorial affair was just the apparent reason, a reason for ethnic russians to vent their anger on their (or not really theirs, because the can't elect it) government.
My best friend married a estonian-russian and ran into endless trouble because of her "alien's passport".
There's some double standard regarding the treatment of russians here.
If any european country would treat, lets say Turks or whatever muslims the way the Baltic states treat Russians, the whole ummah, every PC politician and half the press would gang up on them. Or remember when Austria elected Haider?
Haider is a choir boy against the leadership of all baltic states regarding nationalism and treatment of foreigners. Seems that racism is ok in the EU as long as it is directed against russians.
So if you don't want to give the russians an excuse for being agressive to you, simply don't treat russians as second class citizens.
The baltic states remind me of the "big dog and mee-too" syndrome...