A description of what I'm going to accomplish:
If you were going to start from scratch, a useful search term would be "tree diff".
There's a pretty awesome blog post here, although I just found it by googling "daisydiff python" so I bet you've already seen it. Besides all the interesting theoretical stuff, he mentions the existence of Logilab's
xmldiff, an open-source XML differ written in Python. That might be a decent starting point — maybe less correct than trying to wrap or reimplement DaisyDiff, but probably easier to get up and running quickly.
There's also html-tree-diff on pypi, which I found via this Quora link: http://www.quora.com/Is-there-any-good-Python-implementation-of-a-tree-diff-algorithm
There's some theoretical stuff about tree diffing at efficient diff algorithm for trees and Levenshtein distance on cstheory.stackexchange.
BTW, just to clarify, you are talking about diffing two DOM trees, but not necessarily rendering the diff/merge back into any particular HTML, right? (EDIT: Right.) A lot of the similarly-worded questions on here are really asking "how can I color deleted lines red and added lines green" or "how can I make matching paragraphs line up visually", skipping right over the theoretical hard part of "how do I diff two DOM trees in the first place" and the practical hard part of "how do I parse possibly malformed HTML into a DOM tree even before that". :)