1. Sam is Julian's daughter and maybe Cyrus is still pissy that Julian botched the bomb's intended target.
This would make no sense. But it's as good a reason as any. I just don't see a good reason for him wanting to kill Sam. Makes no sense.
2. Eliminated Sam would remove an obstacle to a Dante/Lulu reunion. Now this would be a total redux of Anthony Z murdering Shiobhan because she was standing in the way of true love--Lucky and Liz reunion.
This would be a ridiculous reason, because like you said, nobody would have thought she was going to wake up. And why was he angling to have moved out of state? Wasn't it North Carolina or something? Isn't that where his mother is or was? I wonder if he wants to take care of Lulu like he wasn't able to do with his mother, who hated him. But the killing Sam part still makes no sense in that scenario. And he's never shown any interest in anything to do with Dante. Why would he want Sonny's son happy with Lulu?
I really feel like it's #2 but even that is ridiculous. Why? Lulu needed the liver transplant because she would have died without it. There was never any indication or hope from the doctors that she would close to waking up. So then why would Cyrus need to remove Sam as an obstacle? If this ends up being the motive, then why wouldn't the writers have Lulu wake up BEFORE Cyrus murdered Sam?
Because KM was fired and having Lulu wake up too fast would negate the reason to kill her, if it's #2.