Always thought with the information that in the 31th century they fight a Temporal cold war that it's like with every war nothing is as it was before.
Why do we believe the Temporal Agents of the Future are protecting the very original timeline? Since the Federation prevails they must have kind of won the war. But as all factions of that temporal war messed with the past to give their faction an advantage and the enemy an disadvantage, I believe the timeline which is protected is not the original one but the one which brought the federation to victory. And we basically don't know which events fall under that timeline.
In first Contact the Enterprise helped to build the first Warp drive since that was what should happen or should it? Did Cochrane invent the Warp drive or was it actually Laforge? Or maybe Laforge build only a slightly better one which paced up the development of the Warp drive in the Federation. Also in Voyager we get to know that a lost Timeship was reverse engineered to develop microchips in the 20th century which had been the past for Voyager already. That was not corrected? Because it is also the past of the future Agents but not of the first timeline. In which all that must have happened much slower.
So my guess is basically that some Temporal Events were tolerated or even willingly guided by the future War Federation to come out on top of all that temporal fighting and then those Events are seen as the correct new timeline which must be secured to ensure victory of the Federation for all times. And maybe the point of Voyager bringing home Future Tech and giving the Federation a huge Tech boost is how it should be and just seems not right to us who always think the Future guys want preserve an unalternated timeline.