The trouble so many have with the Valley isn't early acquisitions per se, it's that so many companies are basically fake. As you yourself explain, in "Hiring is Obsolete", many companies wind up being something the founders do to prove their worth as big company employees, rather than something that might someday make money. A huge fraction of acquisitions are shut down afterwards - pretty conclusive proof the "company" (the software, product, business model and sales channels) has negligible value.

Of course, as you've also pointed out, such "HR exits" are a small fraction of your and other VCs' returns. However, if they predominate numerically - if 80%, say, of YC companies are "acquihired" - this will inevitably affect the character of both YC and its applicants, making it more similar to just another recruiting agency. When our brains assess the character of a place, they weight by "number of people I've talked to", not "market value at exit".