You could also create the ePub using the MultiMarkdown tool for doing so.
I think that is a much better start than a single HTML file, though Sigil does do a pretty good job of taking a well-formed HTML file and turning it into an ePub file.
Now, as for using Scrivener’s rich text editing tools and rulers for MMD, as you not that isn’t really possible—though you can actually achieve a bit of a balance here, depending on how much formatting you need. For example in the Transformations compile pane you will an option “Convert to plain text”, where you can change paragraph spacing into real newlines. So with that way of working, you would use paragraph spacing in your editor while writing, most likely switching things back to indents using the Formatting pane when producing a rich text document, but when compiling to LaTeX you could flip this option on to get real paragraphs.
Another option in the Transformations pane that lets you work hybrid a bit is the “Convert Markdown to bold and italics”. As it sounds, this only does basic Markdown style formatting to rich text, it is not a full MMD parser. So if your intended ePub has extensive use of formatting this won’t be a total solution.
Finally, consider that images, footnotes and titles can also be intelligently handled by Scrivener per-format. It will turn these things into MMD syntax if needed, or rich text formats and conventions for ePub.
As noted above, Replacements can also do you a lot of good, especially now that they are RegEx capable. You can search for [b]^>\s?[/b], replacing it with nothing, to strip out an MMD block quote signifier. If the base text that had that signifier attach is also block indented using rich text, then you can compile to LaTeX with the “> ” signifier, and use a replacement to strip it out for ePub, using the visual indenting to suffice as quotation indication.
Ultimately I agree with your final conclusion though. It will be easiest to take full advantage of MMD’s syntax, rather than adopting a hybrid workflow, and since it is not impossible to get an ePub file out with MMD, and ePub files can in turn be turned into Mobi files, there aren’t many downsides to taking that option if you are comfortable with it.
Make sure you have the RegEx checkbox enabled for the replacement row. If you do not see that checkbox, you must be using an older version of Scrivener or Mac OS X. You can still do newline replacements though, just use the Option key to insert whitespace characters. It’s a little unwieldy though.
As I say above, if you want to take a hybrid approach, it is much better to use visual paragraph spacing in the editor, the Transformations tool for when you need literal spaces (LaTeX), and the Formatting pane to convert paragraph spacing to indents for traditional publishing. That will be less error-prone than global carriage return search & replace, too.