I don't think there have been any realtime 4X strategy games that don't let you give orders while paused. Because that's the whole point of the pause, to let you manage the whole thing.

As far back as I can think, to Remember Tomorrow and Imperium Galactica II, realtime 4X games let you give orders while paused.

Adding to these and the other games mentioned in the thread, Star Ruler 2 is a great game that's free (open source, even), StarDrive sort of fizzled out but you can look for the StarDrive-Blackbox project that aims to revive it, and if you're not much into reading russian to play Remember Tomorrow, the game got remade and updated as Polaris Sector.