I suggest creating a new mission type for identifying and pinpointing XCom bases, followed by a base invasion mission. Or if you guys don't think that's worth it, creating a search and destroy mission to do both in one. They were foolish enough to tip us off to their missiles base so we may as well make the most of it.
That'd be a design, I think. We're on revisions at the moment.
If we want to counter their missiles, I can think of several options. Like these two:
Defensive Plasma Wave: Our plasma turrets can be reworked to serve as an anti-missile measure. By simply not applying a strong enough bond to the expelled plasma, it will, rather than travelling as a single blast, spread out from the turret like a wave. Though this diffuse plasma is unlikely to cause serious damage to larger craft, it should be enough to detonate missiles.
On detecting incoming missiles, our vessels will turn all available turrets (or the ship itself) to face them, and unleash the plasma wave. This may not destroy all missiles, but it should reduce their number considerably.
Reinforced Craft: When we came to this world, we were not expecting stiff opposition. As such, our craft are ill-equipped to deal with the Earthling's missiles. Their hulls are paper-thin, their internals fragile. Simply adding an extra layer of Alloy onto our hulls, and around critical components, will drastically increase survivability in the face of a missile attack.
PPE: EFP is good, but I worry it might increase the cost of our craft.