I disagree that Vol'jin's missive to Jaina either legitimizes her conduct or serves as any kind of surrender or appeasement to the Alliance by proxy - it's basically one leader telling another "you've got reasons to be angry and those reasons are justified, but the one you're truly angry at lies imprisoned and awaiting justice even now" also adding a healthy dose of "you were a woman of peace once, and the world needs that now more than ever" guilt-tripping. I won't say it's a paragon of statecraft on Vol'jin's part, but it's a far cry from a blunder or a misstep.
As for the mana bomb thing? I don't think the existence or manufacture of mana bombs is a state secret of any kind - and I'm sure both the Alliance and Horde have equivalent devices at the ready. Theramore as an event was more about the use of the Focusing Iris, itself property of a neutral party, the Blue Dragonflight, to create what is effectively the Warcraft parallel to a WMD and then unleashing *that* on Theramore proper. It wasn't about the specific type of ordinance employed, but rather the sheer scale and destructive capability of said ordinance in a world not ready for war on that level (and in terms of escalation it was a huge jump from the relatively minor skirmishes that had come before it).