Those were isolated incidents. They certainly weren't something Western leaders gave much thought to (the fact that Clinton had numerous chances to kill Bin Laden but refused to pull the trigger to avoid diplomatic fallout proves as much).
Political leaders represent the state. Military leaders do as well, but to a lesser extent. According to Western rules of diplomacy, sovereignty can only be violated in times of war, and even then representatives of the state should be immune from being targeted. Otherwise, wars would never end. Scientists aren't sovereign representatives. Plus presumably the Europeans think that if they say nothing about Israel taking out the scientists, Israel won't take more extreme measures.