1. She's threatening to tell all. Deb regrets killing LaGuerta, and she seems like she's desperately seeking some form of redemption. But coming clean about LaGuerta's death would bring Dexter under scrutiny. Dexter has killed to keep his secret in the past.
2. Dr. Vogel might make him. Dexter's mother figure seems to be gaining a hold over his actions, and she might manipulate Dex into killing Deborah, simply to ensure that Dexter stays by her side and protects her.
3. He's killed innocents before. Deb isn't exactly pure and innocent, but Dexter has killed people more innocent than Deb in the past. Relative innocents Clint McKay, Stan Liddy, and Jonathan Farrow were arguably less deserving of death than Deb.
4. She's out of control and unpredictable. That makes her a threat to herself, Dexter, and potentially even Harrison. Mess with Dexter's kid and you get killed.
5. It's merciful. Dex has already pointed out that the Deb he knew is dead. The Deb fans see in Season 8 is violent, impulsive, and dangerous in a way that Season 7 Deb just wasn't. She's clearly exhibiting some self-destructive tendencies, and Dex could put her out of her misery. Hey, he did it for Mrs. Figg.
1. She doesn't fit the code. Dexter has proven over the years that he can show restraint in killing the most dangerous of people, simply because they don't fit the Code of Harry. Doakes, Ellen Wolf, and Lumen Pierce are all examples of Dexter being able to control his urges.
2. He loves her above all others. While Dex may not share the romantic feelings that his adopted sister has for him, he has repeatedly expressed his platonic love for his sister. He could never strap her to a table.
3. He can't afford the heat from Miami Metro. If Deb turns up dead, all eyes turn to Dexter, either as a suspect or as a key forensic investigator. Dex is a good actor, but is he that good?
4. He will need an ally against Hannah McKay. Hannah's coming back this season, and she'll undoubtedly have an ax to grind. Deb and Dex will need to band together to stay safe from this master poisoner.
5. Spinoff potential. There have been rumors for months now suggesting that Deb may get her own spinoff series once "Dexter" is over. If Dex kills Deb, then the spinoff is DOA.