First point: realism. Apart from catapult and Casablanca such attacks didn't happen for a reason. The reasons are heavily defended warports and that one simply can't place a surface fleet in striking range without the enemy's notice; there are many other ships and boats trafficing and of course patrols. Next point is retaliation, both french fleets returned fire.
Stacking isn't an issue at all, because you can move, attack, and move again.
Next point: balancing. Until my latest games just a few of my opponents used their RN and french ships to attack the RM in their ports, if they tried to they weren't successfull, except the latests attempts. Allthough I think the player should be able to use the french fleet at his will, the surviving of the RM shouldn't be a matter of good or bad luck like the 10-20% chance of collateral damage. There's no realistic way to protect the RM other than to place them in ports, and no possibility to provide air cover against 4-5 cvs.
The whole naval combat needs an urgent overhaul, the issue is that a fleet itself isn't able to scout. Extend the scouting range of coastal regions to 3, and give the smaller vessels more scouting range according to their size. That's what they're for, screening.