John Doe planned this meticulously for a very long time, and with the exception of that small glitch where Somerset and Mills find his apartment a bit too early, it's safe to say his plan is carried out. However, Doe's plan involves 7 victims representing each sin, but not necessarily performing them or dying for them:
- The Gluttony victim was indeed killed by Doe for his sin by being force-fed.
- The Greed victim was killed somewhat indirectly by Doe, also for embodying his sin.
- The Pride victim also embodied her sin, but was presumably faced with a choice and chose death herself. It's not made entirely clear in the film, but it's possible she could've lived. It's also possible that this one was rushed or improvised after Doe was tracked down by Somerset and Mills and had to change his plans.
- The Sloth victim was punished for his sin as well, but he's not dead yet (although braindead and basically a living corpse). His sin of Sloth was also rather forced upon him by Doe.
- The Lust victim was the prostitute, but the guy who actually embodies the sin of Lust is still alive (although traumatized and branded for life for killing her).
- The Envy victim is Mills' wife, although the sin's perpetrator is Doe himself.
- The Wrath victim is Doe, now with Mills embodying the sin and suffering the consequences.
As you can see, the master plan was never as straight forward as '7 people dying for their sins' but rather a complex admonition involving 7 victims and the 7 deadly sins, that eventually loops in on itself (with Doe and Mills playing a part in it: Doe being envious because he's unable to live a normal life in the sick world he's in, and Mills representing the law's inability to cure it). Doe wanted his master plan to be "puzzled over and studied", and now, as Somerset realizes, he's certainly going to achieve that.