If the system involved bouncing the signal around with repeater stations or relays, I would assume Section 31 (or at least Starfleet Intelligence) would have some setup in Klingon Space to monitor their movements. Khan could bounce the signal of one of those as it be logical to have at least two beyond Qu'onos so Starfleet could always see what is going on in that system (or at least spot ship movements regardless of where the planet it in the system...can't have them use the planetary shadow or star as a way to jump ships out of the system to regroup for an assault on the Federation). That is, if they use relays, rather than Scott's setup uses some other form of subspace were the universe is practically smaller, thus not needing a relay as, to the transporter pad, the planet is within 40,000 km or whatever the limit is.
Actually he has exactly ZERO chance of that: Omega Leonis (the given location of the Klingon homeworld) isn't on the ecliptic and wouldn't be in conjunction with any of the planets in the solar system EVER. If in the real world that star has a system of planets, it's also very unlikely that the plane of their orbits is directly perpendicular to Earth at any given time. In other words, it is incredibly unlikely that Kronos could ever be "behind" its own star relative to Earth and IMPOSSIBLE for the Sun to actually be in its way. It needs to be remembered that most planetary systems don't orbit along the same plane, we simply lack the means to DETECT planetary systems whose orbital planes are at oblique or right angles to Earth (since all of our detection methods depend on either doppler shift or light curve anomalies, either of which requires a star's companion to be orbiting in a plane almost perpendicular to the telescope). And even if both systems orbited along the exact same plane with each other (the chances of which are astronomically small) the tiny cross section of their respective planets means that the direct line of sight from Earth to Kronos would probably only become blocked during rare conjunctions once every couple of decades when the planets line up JUST SO to block each other. This, of course, ignores the fact that Khan "planet hopped" through dozens of relays to get from Earth to Kronos. He doesn't actually need a direct line of sight, he just needs his escape route not to have been discovered by anyone until after he's used it.
If warp ramming were practical then it's the kind of thing we would have seen by now, at least by accident. Objects in a warp field aren't actual moving, it's the field which is moving, so an object at warp only has its sub-light energy prior to engaging the warp field. It should be possible to build up sub-light velocity while in the field, using thrusters and impulse engines, since a ship generating the warp field cannot outrun its own warp field; it will always be centered on the generating ship. However, a warp based magnetic gun would be useful anyway. Accelerate the round to an arbitrary sub-light speed, then form a warp field around it as it leaves the muzzle. The warp field allows the round to approuch targets faster than light, extending its effective range, without actually increasing its impact energy. Since Starships are supposed to have effective combat ranges of 100,000 km and more it is the only way an unguided projectile could possibly be practical. There is still one issue. We don't know if the navigational deflector would just deflect projectiles, even if they are coming at warp. There's not much difference between an at-warp ship deflecting sub-light matter, and a sub-warp ship deflecting at-warp matter. If both the projectile and ship are going to intercept head on, then the deflector might have trouble deflecting the shot. Torpedoes are powered and guided, so they get around the range and deflection issues.