I'm saying that punctuation has already solved this problem with the semi-colon. If you have two sentences where the second follows the other so closely that there is barely a breath in between, use a semi-colon rather than a stop. You convey both meaning and flow at the same time, and you keep the grammaticasters happy.
Ah, I love semicolons -- but they're not always as aesthetic as commas (and vice-versa). I find this is mostly a question of overall style and context (the more pretentious the text, the more out of place the semicolon; unless you're aspiring to be a pretentious (post-)modern text -- then the semicolon wins).
You're saying (and I tend to agree with you) that written punctuation is about meaning, and not about where a speaker would pause to take a breath.
Can these two be kludged into a unified meaning? "Write better so that your written words sound good when spoken"?