Just a few comments.
1. Fire control should be detected by the unit targeted if that unit has EM sensors, regardless of the range of the sensors you can't miss you're being painted. At the same time any other ship in the task group would be informed, "hey boys someone just hull mapped us and we have high resolution scanning, setting condition orange."
2. Given the ranges of missiles and the speed of ships, no missile could hit anything not actively painted for the whole missile flight time. Unless you have active (not passive as they would be useless to a missile) systems on the missile itself the missiles CEP would be huge just because frankly in a few seconds the ships move well in excess of a 1000 km. Active sensors on the missiles would allow for way points and last moment targeting (less for detection of where but of determination by the missile of which target to hit). I have missiles with flight times of 130 minutes against even a merchant moving at 700 km/s the sphere the ship could inhabit is huge.
3. No modern navy leaves ships un-engaged, infact no navy has ever done that. There are exceptions if your strike package is too small you prioritize but basicaly no one does the standard tactic in games of firing on one target till it pops and then switching. The reason is that the crews of ships not engaged are much more effective (they are in a far less stressful situation). You could add that the crew bonus of any unengaged ship goes up by +25% (as in add 25% to it not multiply by 1.25). By the way that is conservative.
4. Passive sensors in space don't yield anywhere near the detail they do on the surface. This is due to range and the fact that in the flight time of the signal the ship moves. So if you are a few million Kms from the target when you pick up its engines the ship could be up to a hundred thousand km away from that position. You are always looking at the past. This does not matter on earth since if the target is a micrometer or so away from where you think it is well its not an issue. Once you have him you start to build a plot but you are always seeing the past. This means for targeting purposes unless the ship never deviates from its exact course and speed you probably don't know exactly where it is. There are exceptions (objects in orbit) but for the most part knowing where something was is not as useful as knowing where it is. Plus without triangulation you would only really know the maximum distance it could be, distance to target requires at least a couple of measurements at different positions. But localization for targetting purposes is just about impossible.
For purposes of the game requiring active sensors on the missile (for active terminal guidance) to use way point targetting makes the most sense. Otherwise missile ambushes are just too easy. If your missile doesn't have active sensors then you have to illuminate the target with your fire control the whole way. I know you want to avoid the issues with target position from light speed sensor systems but I think you have to make a break from what is currently the use of an exploit of this. Basically the current way point tactic exploits the game mechanics, so I think you need to add in game mechanics to keep things balanced. Illuminating the target for the last 5 s or so would be pointless in reality, it would also be hard to do since you would not know exactly where your missiles where, nor exactly where the target was so timing it would be harsh.
I hope this makes sense.