The Elite Missile Tower is probably one of the most hardest buildings/structures to deal with, even an elite sniper can't destroy it easily because of the sniper having the same range of the missile tower.
Strategies to take it out:
-Use a rocket battery to get close to the tower, fire two rounds of missiles, and then retreat to a safe zone. You know when you have to move due to a new batch of rockets appearing in the missile tower`s loading bays.
-Ask your allies to mortar strike the tower.
-Use your Orbital Laser fire call to destroy the Tower. If you use this, you will need to keep in mind that you will need to keep collecting parts for it to be fired.