I think the main problem is that players will probably expect to get some feedback from the GUI when issuing commands while paused. E.g. if you click to train a dozen units, you'd expect to see your resource counters go down, so you can tell when you've spent all resources. We don't currently have a good way to implement that - your commands don't get executed until the next simulation turn (so they'll never get executed while the game is paused), and the GUI just reflects the current simulation state, so we can't update the resource counters while paused. I'm not sure how we could cleanly fix that, and it's easier to just prevent the player issuing commands while paused.
But there's no technical problem other than the GUI - you can open the console (F9) and enter Engine.SetSimRate(0) to pause the game and close the console and issue some commands then Engine.SetSimRate(1) to resume, to see what the behaviour is like.