Sorry to sound harsh, but a keybind is the solution, and it is in game. You are asking the devs to give attention to something so you can leave your torps on auto-fire? What if another player prefers that the Omega fires first as it currently does? Should they lobby the devs to get it changed back? It's your personal preference that they fire in a certain order, and the tools exist to allow you to control that order.
While I suppose that's fair enough of a point, I'd add 2 things:
1. By any measure, the new OMEGA and Romulan space sets were undertested... they have many things to be worked out (for instance, the way the torp works now was just to stop an exploit on the test server with people shooting all five charges as THY or TS). Also, consider that the omega weapon 3-piece set bonus is (by all appearances) nonfunctional as is the Romulan Plasma torpedo launcher (it's just a placeholder). Now is the best time for people to express their concerns with how it works.
2. Because the mechanism for this torpedo is different from other torpedos, it might make sense for it to not trigger GCD of normal torpedo launchers.