Wait, wait, wait...you're saying that because a missile has shot down a plane before in another country during a conflict, the United States military is firing cruise missiles without clearing civilian airspace?
Malaysia Airlines Flight 17 was shot down with a surface-to-air missile, a weapon intended specifically for targeting aircraft. A "cruise missile" by comparison is intended for terrestrial targets and has a minimum range of a few hundred miles. Should the missile come in contact with an aircraft during its initial launch phase, your warhead would basically come right back down on top of you - which is why they close the airspace.
This is reference to this incident that happened during peacetime in 2001 - not later incident during the conflict.