It seems too obvious that he is her father so hopefully he isn't. Maybe her husband is the biggest fish on the list.
Based on the clues from the last episode and from the pilot, in the writing and the way it's written, it appears that
- Elizabeth Keane's father is actually still alive
- Raymond Reddington and Keane's father are not the same person
- Raymond Reddington and Keane's father are enemies, both are high level criminals
- Keane's father is responsible for the death of someone Reddington loves
- Reddington is using the "list" as revenge for anyone associated with Keane's father who was involved in the death/coverup
- Keane's father is dying, needs a massive amount of organ transplants, and the only way to farm them is to get harvest them from Keane
- The "husband" works for Keane's father, his job is to protect her and keep her "body" safe, and also to get her pregnant, as he needs the stem cells to recover.
- Reddington wants to use Keane to wipe out her father's contacts on that list, then use Keane as his main point of revenge. He's only "protecting her" in so much as he wants to save her for his end game.
- Writing convention will generally dictate that the death that pushes Keane is of his own daughter, and that Keane becomes his surrogate daughter over time, which drives the conflict in him about what he is doing.