Well…
There was, supposedly, an ending where that was a choice. Since all of the entities, mostly Subject: 009 or “Jeremy”, were about the Facility doing what they please, the player has a choice to nuke the place and prevent the entities from escaping the place as well. Or you could escape and have the risk of an entity following you out.
When the nuke goes off, you can’t really run from it at that point, so you sacrifice yourself only to keep the world at peace.