I tend to agree with you. I will be evaluating the private beta of "Beer SE" soon, and this is what has become evident to me as I watch this site develop:
My Beer SE Evaluation
The cross-cultural interests between "Homebrew SE" and "Beer SE" have way more overlap than I would have anticipated. I am not typically an advocate for combining producers and end users, but in this case, there is simply too much overlap of interests — not necessarily physical audiences, but interests — to ignore.
Hypothetically, if we were to remove the "brewing-related questions" from Beer SE (I'm not suggesting that), this site would become one big snooze fest fast. After I figure out what temperature to keep my beer… and how to keep it going skunky, just about the only interesting questions left are those that DO veer into what goes behind the brewing process. The deeper "consumers" here are asking about the "artisanship"… and that's the best part of this site.
It makes sense, really. When there's a fervent appreciation for a subject (at least food/drink space), the more-engaged experts almost have to delve behind the scenes to study what separates good brews from bad; to understand the parameters that go into what they're "appreciating."
You don't have to be a literal "brewer/craftsman" to have an implicit interest in the subject. Many of the beer enthusiasts here are curious about the craft — you almost have to, to appreciate the subject — and that's why they are asking about it here. And of course the craftsmen need to know what makes a good beer … so there's a lot of cross-cultural interests here, whether you an actual, literal "home brewer" not.
It simply makes sense to combine these subjects. While the brewers and consumers are not physically the same exact audience, they do largely seem to have the same range of interests… and questions. Essentially, the scope of these two sites overlap considerably; much more than I would have anticipated.

Put them back together. They will be stronger in combining their expertise; stronger for sharing their mutual interests and appreciation for the subject.