I am going through a Voyager rewatch at the moment and I hit the two parter where they go back to 1996. Was thinking about this a bunch. Here’s my headcanon.

The Temporal Police exists to make sure a the timeline is kept consistent. Any random deviations that occur are problems that must be corrected and they’re usually fixed with zero hesitation. However certain deviations are considered “legitimate” for a whole host of different reasons. Some are for paradoxical reasons like needing time travel to be created/used in order to make sure the Temporal Police are created. Others are okayed because the Temporal Police are the ‘victors’ that write history and get to choose the good things and leave behind the bad. Then there are countless other reasons.

When it came to Admiral Janeway, she fell under the two main categories I mentioned. The first is that her actions in using this time travel tech was integral to the creation of the Temporal Police. Could be something as simple as this being a case study in why such a police force was needed. In which case you couldn’t police it or wipe yourself out in a paradox. The other is that her actions greatly benefited the timeline. The Borg were an enormous threat and by going back in time and annihilating them, she made the timeline safer for all Temporal Agents.

tl;dr They couldn’t stop her because she timetraveled so hard she’s the reason the Police were even created