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.