I've been tooling around with the same idea. I agree the current trajectory is a little strange and a ballistic trajectory would spice things up.
I wasn't aware SMDs could intercept missiles mid-flight as is, but was going to recommend it. SMDs can intercept missiles of an arbitrary height if you add MaxHeightDiff to their weapon blueprints ("changes the weapon range from spherical to cylindrical, where the cylinder has a height of this twice this value"). That may or not work as stated given that no units currently use it.
This could be tweaked so SMDs could intercept missiles only in the "boost" and re-entry phase (or even allow smaller, less capable SMDs to be added...!), but not at the highest point of their trajectory, which has a certain je ne sais quoi.