If we had started with 'full' media from the beginning we'd still be describing and making media variants rather than getting any cancer research done. And we've done a hell of a lot of good cancer research since these media were defined. It's a little like the 'Standards' xkcd comic - if you make too many standards, the standards cease to be useful as a standard.
Further, the effect of the media in this case here is likely more profound when doing 'biology' rather than 'biochemistry' experiments. And until recently, the cells themselves were toeholds onto real human biology; HeLa cells are very unusual, but we used them because we could reproduce the work between labs because the cells proliferated indefinitely. Who cares about a little unnatural media when the genomes of the cells are completely messed up. (And again, the use of HeLa cells taught us a LOT even if they were very not-normal). Normal human cells just don't last outside of a body - so if one insisted we only use normal human cells there would be zero research, and even less reproducible research because no one could use the same stocks.
It's only and precisely because we do have a (admittedly flawed) standard that such a different and likely more natural media even can be objectively compared against.
Biology has a lot of variables. You can't hold everything constant the way you'd like. So you pick just those that you expect will make the biggest differences. And we should certainly go back and check ourselves every once in a while to ensure we don't get lazy and assume a particular protocol should remain the same in the face of changes in the field. But I don't think that's the problem here. We're just better scientists now - and we're learning that our early assumptions can now be improved on.
The article, especially in its final paragraphs is actually quite even handed. The title, however, is very much hyperbole.