The problem is that sage actually depends on Octave, Maxima, R and many other packages. It parses binary output of many dependencies and often needs the exact version it expects because of that. It also has relatively brittle doctests testing everything an as a result often breaking on minor changes in dependencies.
I recently started using Markor for that purpose. While it wasn't built as a vimwiki client, it is good enough for my purposes. Some info at https://github.com/gsantner/markor/issues/317.