Voyager getting home ahead of schedule "reboots" the future. The Admiral Janeway we saw thus became a temporal paradox. Her death only cleaned things up, removing the last traces of the other timeline.
That's the great thing about this kind of time travel... you change the past and then the "new future" wouldn't have any clue about the change.
But then you have the USS Relativity with all of it's time line continuum scanning... wouldn't they have detected this breach of protocol and tried to stop her? Well, that would put too much of a burden on the premise of that episode. Suffice it to say, they probably saw that there was more of a benefit than a detriment, and allowed it to take place.
That's the great thing about this kind of time travel... you change the past and then the "new future" wouldn't have any clue about the change.
But then you have the USS Relativity with all of it's time line continuum scanning... wouldn't they have detected this breach of protocol and tried to stop her? Well, that would put too much of a burden on the premise of that episode. Suffice it to say, they probably saw that there was more of a benefit than a detriment, and allowed it to take place.