Since I'm like 99.9% sure this wasn't addressed in canon (and perhaps 95-98% sure it wasn't addressed in the non-canon novels), here's some theory:
When the future isn't a certainty, it's treated as a whole slew of possible futures, the likelihood of each fluctuating from moment to moment as people take action and make decisions. (ENT 3x23, Countdown, or 3x24, Zero Hour, when the Sphere Builders are examining the possible futures. I forget which one it's in.)
The Federation temporal agents from the future appear to only come from one possible future. It's hard to give an exact reference, since it's strongly implied throughout Enterprise that the temporal agents are working to keep history on-track for the Federation seen in TOS/TNG/DS9/VOY - because it's part of their history.
Therefore, within these fluctuating futures, the temporal prime directive had to have come into effect in at least one of them (since there are infinite possibilities). Since that future came into existence, they would have been working to keep history on-track so that they continue to exist.
Given the above, it would seem that if Voyager took those extra decades to get back to Earth, something would happen in the intervening centuries that prevented the Temporal Prime Directive from coming into effect*. So there's one possibility: There were no temporal agents in that timeline to keep her from going back, and in the prime timeline Admiral Janeway was part of their history.
*This goes beyond theory and into speculation: Think of how Admiral Janeway's plan affected the Borg. I suspect they mounted some sort of attack on the Federation in the Admiral's timeline after her time, but before the temporal agents came into existence. But in the prime timeline, Voyager was able to get Seven of Nine, the Doctor's mobile emitter, specs for the quantum slipstream drive, and whatever else they picked up, to the Federation decades earlier, likely causing a jump in their technology, and the Admiral caused tons of damage to the Collective. The attack, if it even happened, was likely thwarted.