I think you misunderstand time-locking. It's discussed in the Wiki link I provided in post 148. Alidar Jarok
has the right of it. They were all killed. The time lock is a barrier that prevents the Doctor from going back to those events to alter the outcome.
Put another way, it's the same reason the Doctor can't go back to Manhattan and retrieve Amy and Rory. It's a plot device to explain why he can't use time travel to fix the problem. The Time War, like 20th-century Manhattan, is inaccessible to the TARDIS. He can't get there, can't save anyone from what happened there. So they're dead to him, just like Amy and Rory are. The difference being that the time lock blocks everyone (with one exception that barely succeeded), not just the Doctor's TARDIS.