Having a finite number of command points is indeed arbitrary, and it bothers me in principle. In practice, however, I have never actually run out of them, so it doesn't affect immersion or freedom.
....During this time, you would have some sort of penalty, the first one I can think of being that your ship idles, or is controlled by your first officier (the AI). It could also take a few seconds for them to receive and react to the order, making "micro" useless and impractical. Either that or add a separate cooldown to each unit on how often you can give them an order, on top of the transmission time.
Losing control of your flagship would be frustrating, and potentially disastrous. Instead, perhaps pausing in the war room could be disabled instead, thus forcing the player to balance their attention between controlling their fleet and their flagship, but this could likely end in catastrophe as well. I wouldn't be surprised if the devs have tried this at some point, and if so, I'd be interested to hear how it went.
Delaying order transmission wouldn't discourage micro, because you can't micro your units. They make their own decisions, and they're quite good at it.
2) Another possible alternative would not get rid of command points but instead make it so that 1 command point allows you to give as many orders as you want at a specific moment. For example you pause, send Bob to retreat, Joe to capture the sensors and Alex to clean the toilets. This is 3 orders but you give them all at once with the game paused so they cost only 1 command point. With this method, each command point represents an entire "decision" or an entire "change of plan" or "next phase of the plan". I think this would already be much better because let's be honest, sending 2 fighters wings somewhere seems petty but costs 2 command points while sending the Bis'mar somewhere is a huge tactical decision that only costs 1 command point. With this method each command point deserves equal thought and is significant, and the amount of command point could be balanced to reflect this.
Again, running out of command points isn't a problem. The problem is that command points are an artificial resource, and your second suggestion doesn't address this.
It'd be like you, as the commander, get on communications occasionally to update your orders for all members of the fleet.
This is how it currently works. You don't give orders to individual units; you give orders to your fleet as a whole, and units are automatically allocated to tasks.