Because "listened" is in the past tense, I'd say that the first sentence would be better as follows:
Though it hurt, Linda still listened to Jeff.
Though it hurt her, Linda still listened to Jeff.
No, the two sentences do not mean the same thing. "Though" suggests that Linda is enduring her pain, and that her pain is directly related to the act of listening to Jeff. That's because "though" is a subordinating conjunction, implying a cause-and-effect relationship between the two clauses. Sentence #1 contains a participial phrase "Hurting", which modifies the subject, Linda, but otherwise doesn't say anything about the rest of the sentence.
Consider that this sentence preceded yours:
Linda's team was losing, and her legs were burning.
Sentence #2 would still make sense. Linda is hurting because her legs are very tired. Perhaps Jeff is her coach shouting instructions from the sidelines.
Sentence #1 makes less sense. We know she is in pain from playing the game. But why does it hurt Linda to listen to Jeff?