If there is a significant delay until the ball can be returned to the player on the endline for a throw-in, then the official should blow the whistle in order to stop the clock. There is absolutely no reason why either team should be penalized by a loss of time in such a circumstance. Remember that the loss of time could also affect the team NOT having the throw-in. This would apply at any stage of the game...even in the first minute of play.
I don't know if there is a specific rule for this, but you can always use Rule 2, Section 3.
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