I was a weapons engineering officer for the Dutch navy for 14 years; I'm well aware of the mechanisms involved. First of all, a SM-2 will not use the flight pa

I was a weapons engineering officer for the Dutch navy for 14 years; I'm well aware of the mechanisms involved. First of all, a SM-2 will not use the flight path you describe as they tend to "dive down" on a sea skimming missile. But even the shorter range Sea Sparrow missiles that do behave as you describe use multiple guidance phases. In the early and mid-phase guidance phases, the radar reflections from the target missile will not be strong enough for the relatively small receiver in the missile, so the system must depend on midcourse guidance updates (little bit to the right, little bit up, etc) from the combat management system on board the launching vessel to navigate to a "close enough" location from where the sensors on board the missile can acquire the target. The end-phase guidance and fuse timings are quite critical, as you say, but they are also not really under command of the CMS but rather done by embedded systems on board the missile. Generation of the mid-course guidance updates is not nearly as time critical and won't suffer much from a 1 ms pause. The error in location estimation of the target due to sensor imperfections (limited angular resolution, clock jitter, athmospheric effects, etc etc) will be way larger than the 2 meter from the GC pause.