Bootstrap paradox.

They found the planet in the state their time travel left it; Chernobyl’d.

Investigating it resulted in the time travel. The time travel resulted in the crew forcing open a rift to get them back. That rift resulted in the explosion in the first place.

So Janeway closed the rift at the last second after putting two and two together. Because the planet-wide explosion never occurred, they never time travelled in the first place.

Instead, they find a happily chugging along pre-warp civilization and just let them be.