That's true. People scoff at the older taxonomic groupings from before we had molecular evidence, but actually I'm often surprised at how similar new phylogenies are to huge chunks of the old taxonomies. What's more, at least with plants, one molecular study can produce quite a different looking evolutionary tree to another depending on what genes they used to compute them.
Which begs the quesiton... what's the ground truth? Data from classical taxonomy is actually extremely valuable. It can help inform molecular studies. It can be used to feed consensus trees or indicate which genes might yield certain phenotypes.
There seems to be many who think that with enough CPU power and algorithms we can turn any old meaningless garbage string of GATC into something we can pretend is useful. It seems like a lossy way of thinking... you can do interesting work without names, that's true - but the reckless abandon and total lack of scientific discipline when using names would never be tolerated in the "harder" sciences.
I dare you to pick up ten different papers using species or group names... and find even just one that cites the name in a reporducible, scientifically useful way (i.e. cites the taxnomic publication which specifies what they mean when they use the name).