genes and memes are not the only alternatives as beneficiaries – there are institutions that can be treated as self-interested agents for purposes of economic, political, sociological, and cultural analysisThat seems like a mixture of levels of explanation. "Institutions" are a mix of genes, memes, gene products, meme products - and maybe some joint meme-gene products. The "products" are phenotypes. In biology, genotypes are what is inherited and phenotypes are everything that is derived from them. From this perspective, only the genes and memes form important lineages and can qualify as beneficiaries. The "products" are more transitory - they are not inherited from they affect gene and meme frequencies via selection, but don't "benefit" because they die without leaving any offspring - and "benefit" in evolutionary theory is measured in terms of fitness. Only genes, memes and other forms of inherited information really qualify.
Of course you can also talk coherently about larger-scale entities benefitting in evolution. An animal might be said to benefit by having offspring. However it is just a different level of explanation. It is quite compatible with the meme's / gene's eye view. It's a lot like saying that their genes benefitted - on average. A focus on low level beneficiaries doesn't somehow exclude higher levels. I think this critique of Miller's doesn't really go anywhere. Meme enthusiasts aren't somehow ignoring institutions. Institutions are composed of memes, genes and their products. You don't need to do fitness accounting on memes, genes and institutions. That would be counting things twice.