No, they aren't. Though, I do consider Bacon and Hodge the leads of the show. I'm just not interested in Siobhan unless she's in her own plot, but I think both hers and Jenny's should be a minimal part of the overall narrative.
I think splitting them wasn't a strong narrative choice for S2. I would have gone with uneasy truce. I take the point that Decourcy kind of was full of himself, and despite Jackie being a sleaze, he was right about putting Jimmy on the stand with the blanket immunity. So it was self-inflicted on Decourcy's part, and kind of tragic. And Jackie did screw up the bust.
I would have liked a time jump (small) with a more Boston-weary Decourcy. With him needing to get out of the doghouse and Jackie needing to placate the new US Attorney, there's plenty of material there. I don't think they would have needed the drug overdose for the Asst. plot. Again, she was snorting up the cocaine like a Hoover. Jackie wasn't forcing it on her.
I was assuming he's kind of in the penalty box for court because of screwing up last season, so he's been relegated to a more investigative role.