I agree with you guys about the scene with Vader force pushing Juno. That was very badly done. He could have easily stripped the saber from her with the force and then choke her for punishment. He needed her alive for Starkiller to follow his orders. What should have happen (and does happen in my mind anyway when I see that scene), Juno grabs Vader's saber like she did, but instead of just pointing it at him, she swings it and clips Vader's side. This causes just superficial wounds but enough for Vader to lash out instinctively with anger and force push Juno with lethal intent.
Now this mystery if Starkiller is really Galen or a clone. Through out the game we see Starkiller show very strong emotional ties to both Juno and Kota. He really cares about them. Then there are the flashbacks that happen during certain events in the game. When doubting that he could be Galen we see a flashback of when Vader brought him back from death's door in part one. Could be just a template memory or it could be a hint that he was brought back after his "death" suggesting that it happened again. In the final fight with Vader, Starkiller tells him, "I've always been stronger than you" in which Vader replies, "and yet you fail to kill me". Was this a slip on his part admitting that Starkiller was in fact Galen and not a clone?
The ending has two parts, one light side and the other dark. Assuming that this sequel follows the same format as the last, the light side ending is canon while the dark side ending is a "what if" scenario. At the conclusion of the light side ending, it looked to me that Vader failed to create a stable clone from Galen and decided to try to convince Galen that he WAS a clone. Then he tried to blackmail him with Juno but that didn't work out either. The dark side ending had Vader successfully creating a stable clone from Galen's DNA. Better yet, this clone fully embraced the dark side, were Galen never did. Then there is the possibility that Starkiller WAS in fact a clone. In this scenario, even if he was, like Kota said, it wouldn't matter. Through the clone, Galen would have been "resurrected". The same thing happen to Star Trek's Spock in "The Search for Spock".