Basically, the only thing the Temporal Prime Directive cares about is ensuring the timeline in which the Federation, KDF, and New Romulus unite into a massive Federation in the future and in which the Temporal Accords are signed into law. Nothing else matters. So if nobody stopped Janeway from doing what she did, it's only because what she did ether helped make that timeline possible or had no effect on it.Why didn't future starfleet try to stop Janeway's obnoxious shattering of temporal law....oh that's right, future starfleet time cops are fucking stupid and make no sense.
Yes, it's a bullshit answer and it's one that the writers at the time didn't know about (because the Temporal Cold War wasn't a thing until Enterprise), but it's the "official" answer.