Is it actually safe to warp into a planet's gravity well, and atmosphere? Plus I'm sure there's plenty of ground-based defences. Humans fight for land, not for space. Maybe some THAADs or PAC-3s or something, then SAMs and maybe shield the top of the missile silo. Would be pretty cheap to shield the lid. It's probably the size of a Vajra.
Well, we thought about this. We figure that the energy required to make a jump depends on how deep you are in a gravity well, and how heavy you are. So while you may be able to jump into a gravity well, you may not be able to jump out again. Basically, fighters can skip the Orbit/Atmosphere interface, heavier ships can't. If you've seen BSG's Return to New Caprica arc, you can imagine what a Destroyer jumping into Atmosphere looks like, only minus the successful jumpout.
And, well, FS is still a universe where the Weber/Heinlein rule is valid, i.e. if you control the orbit, you control the planet, because nothing can stop you from dropping ordnance or troops from a superior position.
To reiterate, Surface-to-Orbit weapons systems are one-shot weapons, you can use them once, but then their effectiveness is nil, because the countermaneuvers are rather easy and obvious.
Also asteroids + Earth = Not what GTVA wants
Nope, it's not what they want. However, it's what they can do, and it's what they will do if pushed hard enough.