There are very few reasons for Israel to fly into a panic over a few hundred protesters and every one of those reasons makes Israel look bad. On top of this, whenever Israel is confronted with a new situation which they consider "threatening" in some way, the odds are very high that some IDF or security goon will open fire. This is a far greater threat to Israel than anything the protesters can do.
Jewish teen sustains moderate wounds in stabbing in Jerusalem; assailant shot by police (Haaretz)
from the article: Israel braces for arrival of hundreds of pro-Palestinian activists