When Clay comes to see Gemma in jail, she tells him they can't look at Jax the same way they saw John Teller, because club has been in desperate times. At the end, she sees Jax arrive with Stahl and watches with sadness as Stahl sets up Jax to die at the hands of his own club, by exposing the deal they made. But Gemma gets some relief after Jax sends her a letter explaining that he was never a rat; the deal was a trap the entire club was in on, and the only reason they didn't tell her was to keep her from being an accessory if things went awry. At the end, it is strongly insinuated, via a letter John wrote his mistress Maureen, that Gemma and Clay are responsible for John Teller's death.

does gemma go to jail in season 3?
yes