I totally agree with you. Markdown is nice as a pretty simple documentation format. It is a good fit for something like a letter, a README or a short tutorial. I you go beyond this level, you are better off with something more powerful like AsciiDoc.
From that point of view, tables should have never been part of Markdown.
Nit: tables are part of github-flavored markdown, not John Gruber's original Markdown.PL, and there's also another table extension syntax for markdown. Apart from that, the point of markdown is that you can drop to plain inline HTML/markup or markup blocks when markdown short syntax is insufficient, such as for complex table layouts. Regular markdown syntax really is made for plain text editing. As such, it would probably make more sense that a visual editor, cool as it looks, targets robust markup serialization (HTML-in-markdown) rather than producing markup shortform syntax IMO (but then again, the plethora of markdown editors may prove me wrong on this one).
It seems like the OP would be better served by CommonMark or any of the alternate implementations which are designed to be more feature complete to solve these kinds of formatting problems.
Regardless, if you want to go down the rat hole of exactly what is Markdown, the only "correct" answer is 'whatever Gruber's 'markdown.pl' does, warts and all'.
From that point of view, tables should have never been part of Markdown.