I don't think any Miyazaki films are meant to be abstract, but if you want to assign imaginary meanings to simple kid's movies then go ahead.
Why aren't you raising a fuss about issues in movies that are actually literal in-universe issues? Why aren't you raising questions about the fact that Ponyo literally destroyed 99% of terrestrial life on Earth because she wanted to eat ham?
That rumour is complete rubbish. Really, the so-called "evidence" is ridiculously easy to debunk by just watching the movie. The sandal? It's similar to Mei's, but not hers. Even Satsuki says it is not hers. The sudden disappearance of shadows? Umm, I certainly saw the girls making shadows even after they supposedly became ghosts. Maybe people should be a little more observant. And at the end of the movie, we see both girls returning to their home... unless you want to also claim that the grandma and the boy Kanta are now also dead. And in the end credits we see the mom coming back home and the girls being quite alive. Heck, even Miyazaki has gone on record to say Totoro isn't some sort of a death god. Seriously, this whole story is just seeing things that aren't there and have never been there. Seems your friend has just swallowed the bait hook, line and sinker.