Chances are they could see what changes would come about from Janeway altering the timeline, just as whatever his name was from the Year of Hell episodes could.
The Time Cops then probably weighed the good of the many (mainly the Federation) versus the good of the few (the Delta quadrant) and felt that everyone was better off with Voyager back in the Alpha quadrant 60 years early.
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I would imagine that, in order for a temporal governing body to effectively function, a baseline timeline or epoch date would have to be established.
Timeline manipulation originating prior to the advent of the Temporal Integrity Commission would have to be considered part of the timeline, and therefore not subject to their laws.
Think of it as temporal ex post facto : timeline manipulation laws cannot be applied to violations that occurred (or originated) prior to the advent of such laws.
For example, according to Memory Alpha, timeship Relativity was from the 29th century.
Any timeline manipulation that occurred prior to the 29th century would have to be considered historical, and therefore not subject to Relativity 's timeline enforcement.
Since Janeway's actions took place during the 24th century, where time travel was not so common a thing that enforcement of laws was necessary, no actions were taken to stop her.
scifi.stackexchange.com/users/2443/Chad Levy
One of the trek books ( DTI: Watching the Clock ) answered this question.
It was a series about the timecops.
They said the galaxy with Janeway's time travel was the only one in which the Borg didn't take control of the whole galaxy.
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I always had it in my head that Relativity only fixed timeline changes if the time traveller was from their time anyway, otherwise they can't detect it as it had already happened before the ship and temporal shields and whatnot were built.
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Before they went back in time, there was probably an investigation, similar to what occurred in the frame story in Trials and Tribble-ations .
At that time, it could have been decided that corrective action was unwarranted.
scifi.stackexchange.com/users/3231/Justin Dearing
In the series finale " Endgame ", a future Admiral Janeway travels 26 years into her past to take the ship and crew through a Borg transwarp hub to the Alpha quadrant.  However, in " Relativity ", Captain Braxton and his timeship tried to prevent and correct any timeline interferences (so-called "temporal disruptions").  Why didn't they travel back in time to fix the paradoxes that Janeway created?
Why didn't the time cops try to stop Janeway when she traveled back in time to rescue Voyager?
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<star-trek><time-travel><star-trek-voyager>
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 They could probably see what changes would come about from Janeway altering the timeline, as was the case in the Year of Hell episodes. Also, in order for a temporal governing body to effectively function, a baseline timeline or epoch date would have to be established. At that time, it could have been decided that corrective action was unwarranted. There is a lot of speculation of what could have been going on behind the scenes i.e the time cops could have seen what Janeways actions were going to bring forth and chose to not act or certain requirements needed to be met for them to to take action or to even know what was going to happen. Though it was stated that the galaxy with Janeway's time travel was the only galaxy where the borg's did not rule the whole galaxy.
There is a lot of speculation of what could have been going on behind the scenes i.e the time cops could have seen what Janeways actions were going to bring forth and chose to not act or certain requirements needed to be met for them to to take action or to even know what was going to happen. The time cops decided not to act, because it was the only time fram where the Borg's  didn't take control of the whole universe.