ORIGINAL: feelotraveller
The 'do not engage' option already exists, at least as a default stance. Unfortunately you can only apply it empire wide at the moment. [:'(]
Ok. With your help, feelotraveller (and by re-reading Resan's and Bingeling's posts - particularly when Resan says "Wouldn't it work to set the "Default Engagement Stance" to something passive?" and Bingeling says "The general case overrides the special case"), I finally found a way to keep my fleets from disobeying my stance orders when playing fully manual. It's not intuitive, as Elliot said above (and now I understand what he meant), but I just tested it, and it works. And, I think I may have found a bug on the process.
The solution is to be found on "Empire Settings->Default Engagement Stances". The game's default (after you install it) is "Engage system targets" for all types of missions (escort, patrol, others), if I'm not mistaken. What happens is that, even if you set a fleet's stance in-game to, let's say, "engage when attacked", when some event happens (an enemy attacks your ships for example), the game reverts the stance to the one set on the global "Default Engagement Stances" settings. So, the game overrides the manual controlled fleet's stance from "engage when attacked" (what I wanted them to do and keep doing) to "engage system targets" (the default I had on the settings).
So, the "bug", I think, is that the game overrides the manual-set stance to the default global one after some event happens, in the example case above, when someone attacked me, the fleet's stance reverted to the game's default (engage system targets), and so, some "rogue" ships decided to go "kamikaze", not because of my orders but because that was what the game has instructed them to do. In my opinion, because I like to have full control of things, I think the game shouldn't override the manually-controlled fleet's stances unless the fleet is set to automated.
So, the solution to achieve a "do not engage" stance (not a specific option at the moment), to force your fleets to follow a stance religiously, is to set the "Empire Settings->Default Engagement Stances" to "no default stance" and then set each fleet to the stance you prefer for each. So, while a "do not engage" stance is not available in the game yet, there is an indirect way to achieve it.
But, please be advised that this solution is for people who like to micromanage their fleets, who like to have full control and play manual. If you like to leave all your fleets automated, you should probably leave the default engagement settings to "engage system targets" or "engage nearby enemies", as the game currently has as default. But, even if you leave your defensive fleets automated, I imagine that you'd want to manually control your attack fleet(s) still, and for that case the only solution I have for you, to have full control over the stances, is to set the "Empire Settings->Default Engagement Stances" to "no default stance".
So, a simple solution, in my view, would be NOT to revert a manually-controlled fleet's stance to the default (as the game does now), but to keep it at the stance the player decided in the first place, and keep that stance religiously. When/if the player decides to re-automate the fleet later, that fleet may assume the default engagement stance by then, but not (never) when it's still in manual mode.
Sorry for the long post, but I shared the OP's frustration of not being able to have full control of my (attack) fleets, and witnessing my fleets going rogue. I hope this has helped him. This discussion has certainly helped me have more fun with the game, and certainly understand it better.
Pirate strongholds are still quite tough, and we have to live with escorts and frigates for most of the Age of Shadows game, because research is Very slow.
