1. Sam is Julian's daughter and maybe Cyrus is still pissy that Julian botched the bomb's intended target.
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.
3. Other
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?