List of ways to not make Turkey care about anti-semitism:
1) Put their ambassador in a lower chair than your diplomats and not have a Turkish flag in the room and do so purposefully in a way that suggests your government has the maturity of a 5 year old.
This whole mess is typical of the Lieberman Foreign Ministry approach to diplomacy, acting as if any state that experiences anti-semitism owes it to Israel to grovel on its knees begging forgiveness. The problem is, most of the time the anti-semitism or even anti-Israel sentiments have nothing to do with the government, and heads of state tend to get resentful when they're expected to apologize...and apologize again...and apologize further. The Lieberman approach plays well in speeches, but does little to actually combat the very serious issue of anti-Semitism. Which means Lieberman is putting politics ahead of actually getting something productive done. Although if you didn't see that one coming, I have some desert in the Negev to sell you (if you're Arab you'll have to sign a loyalty oath before we make any deals).
Frustration about the pervasive nature of anti-Semitism is understandable, but this is international diplomacy and there are rules. Snubbing ambassadors is not an effective way to deal with anti-Semitism, it's arrogant and just plain rude.