The 1411 is an admin tool, if a player does not heed a moderators warning, they can use it to get a players attention. If getting shot does not get their attention and the player continues their behavior then a temporary kick or even ban may follow, depending on the severity of the offence.
In this specific case, the engineer turtling reached a point where no action the attacking team could do would suffice to break the door down. The moderator issued warnings while this was going on and acted only in the last minutes to break the stalemate.
Overzealous door repairing that makes it impossible to destroy it no matter the actions taken is considered exploitation of a bug and will be moderated until a patch is released. The engineers did not receive any punishment, it was just the number of them that reached a critical mass.
Every moderation action is also logged and can be viewed by other moderators and developers to be reviewed.