I've been to said area and don't really think the people working there did it either on purpose or mistake. I just think they plain didn't do it.
If you explore the area and learned what happen there you can see some people AFTER the bomb drop tried to launch one and it had no warhead attached - and what they were doing in that base BEFORE the blast was trying to get the IMBs and warheads to fit together - seems they didn't. I don't think they had missiles ready at firing capability. and well, considering where crater of Atom is they certainly didn't accidentally blow one up on site, or that would be the center of explosion instead.
I also find it hard to believe they'd be willing to drop a nuke so close to a stockpile containing numerous more nukes - even if it is in a protected bunker. Just seems like a bad idea.
Also fun note - bringing a companion to that place was the worst choice of my life... "Holy S**t are those missile" literally 2 steps into the door and missiles NOWHERE in sight, basically spoiled the purpose of the whole site two steps in the door. Thanks inconsiderate Bethesda companions.
The issue actually has an answer in the game and is confirmably answered.
I don't think that was supposed to be a secret given that's a missile launching silo.
Companions never watched the trailers. This is the first they've seen the player character's amazing behind.
I had no idea of that going in. To me it looked like a crazy pyramid. I haven't ever seen a missile launch silo like that irl so I don't know. Especially in media usually when you see a launch site it's just a small circle above ground, no a full scale pyramid It would have been nice to figure out on my own what was happening the area but eh, I know it wasn't a major spoiler - just kind of an inconvenient companion moment.