You can. Go to WeaponObject.ini and find the cruise missile then remove UNATTACKABLE and replace with PROJECTILE and SMALL_MISSILE
To set Avenger can using a turret laser on it's back to shoot down the cruise missile. You have to change the KindOf from ProjectileArmor to any Aircraft armor that able to take damage from SMALL_ARMS damage type.
If you don't change the armor type it's more likely the turret back won't shoot the cruise missile or Avenger may use PointDefenseLaser system instead.
This will allow any unit that able to shoot small missile to shoot down the cruise missile.
If you set KindOf to AIRCRAFT anything that can shoot aircraft like MissileDefender, TunnelDefender will be able to shoot the missile too.
Personally I would allowed only big stuff that able to get to Cruise Missile. I would be so weird if Infantry can destroy a big missile