How to filter Named Entity Recognition results
The most advanced (and complicated) approach to this is some sort of weakly-supervised system like Holoclean. It seems promising, but not easy.

The other end of the spectrum are heuristics like the one you propose. If you want to use a string distance approach like you describe, I would create some metric that gives points for both string edit distance and having matching words. If you can break the pipeline into smaller steps, maybe you can use some sort of topic analysis, then look for two similar entities and that topic in a knowledge graph, and see if the point to the same area.

The 2018 Alexa Prize winner paper, Gunrock is full of clever heuristics that you might be able appropriate.

Edit: you should also look at Entity Linking, which is more or less the problem you describe.