When a NATO country sits back and is willing to let a massacre of fellow human beings take place then all protest is justified. Turkey is a country that wants to become part of the EU and EU values do not support sitting back and letting people die infront of their noses.
There may be understandable large political differences but evil should not be allowed to succeed. The protest is justifiable on the basis that the regime is being negligent to basic humanitarian needs.
Its not for people outside of Turkey to discuss and reflect upon whether or not their protests were justified: its their country. Protests in a country are almost always justified; if the people of a country feel unhappy with how things are, and want things to change, they have every right to protest.
While I don't want to see violence arise from these protests it sounds like the protesters may have a point in how they feel they were treated during the urban development sit in they held. It seems like the protests really didn't need to come to this point and could have been resolved if they had been treated better.
What they have done is removing cobblestones, obstructing traffic, reviling prime minister,undermining the prestige of Turkey and etc.. And the reason was dropping the government. As you know, in the Democratic countries, There are elections to determine the government. But they prefer anti-democratical ways to do so. Therefore, of course, what they have done is not justified.