I agree with your proposal. Well, maybe not the part about not letting ships shoot in battle...they will shoot or not shoot based on their proximity to an eligible target and their own classification (support, etc.).
I've always thought it looked odd that GalCiv has always had weapons with muzzles didn't "aim" before shooting. So you could have a dorsal-mounted beam or projectile weapon that would shoot sideways at its target. Ugh! I get it that the animation is not necessarily easy on this, but come on. It's not GalCiv or GC2 anymore. If my home defense firearm shot bullets sideways, the resulting breach in the firearm would kill me or at least maim my shooting hand.
The only weapons that might not need to "aim" are those weapons that have target-acquiring ordinance (missiles that can change direction, for example). Or maybe some beam weapons that have no discernible "muzzle". I'm thinking about the phaser emitters on the Star Trek: Next Generation's Enterprise D. That ship had two big phaser rings; one each around the dorsal and ventral surfaces of the saucer section (and linear emitters on the other hulls too that we rarely/never saw deployed) that could emit single or multiple phaser beams and those beams could move along that emitter.
So yeah, I guess maybe I'm asking for a "little bit" more realism in how some weapons appear during battles. 
