There are multiple reasons why i do not believe that we have witnessed Liberio's destruction. In this post i will elaborate on 3 of them.
1. It does not resemble Liberio. Liberio possesses a very established port, far enough away from land that Armin took a bit of time to get into the heat of battle in the Raid. There is a river running through the town, which we do not see in the refugee kids' perspective from the hilltop. Lastly, there is no segregated ghetto holding the Internment zone.
2. Liberio being closer to Paradis than Seaside Town. This is honestly the wakest link in this theory, but i'll go on it. Liberio is home to the command center of the Warriors unit, so it would strategically make sense that it would be closer to Paradis than the small town, as Liberio was the staging ground for the Paradis Island Operation. It also does not help that it has a significant minority of Eldians, Why do these two points matter? Because the Survey Corps had to infiltrate Marley to gather intelligence. It would be more secretive if they went to a small town with less surveillance against Eldians, far away from any military operatives that might recognize the infiltrators. They weren't after military secrets either, just the basics of Marleyan society and technology. This is why they were able to get away acting like simple country folk who have never seen a car.
3. We would've seen the annihilation of Liberio's inhabitants. Many notable supporting characters, such as the Brauns, Mr. Leonhart, Grandpa Yeager, the remaining Tyburs, all live in Liberio. If they were doomed already we probably would've seen it by now. And honestly, if we won't see their doom then we might've seen Liberio's destruction anyways. The first town that the Rumbling annihilated has more features similar to Liberio (Size, extensive accomodations for shipping) than the town the Survey Corps infiltrated. It might also be one of the towns destroyed in Eren's fantasy sequence (although it's probably still the Seaside town getting demolished).