I've been thinking about this for a while, and I'm not sure it would be possible. Large parts of Sigil depend on the HTML documents being valid XML (thus XHTML). Tidy makes sure that's always true.
What I could provide is an option to turn off the "clean" switch for Tidy. I'm guessing that's causing most of your problems.
And AFAIK I fixed the
span spaces bug. Do you have reason to believe it has resurfaced?