Why are so people so fast to trust a new compiler?
Have you audited that compiler's source and building the compiler from it with a known good compiler? Are you inspecting the resulting .pyc, and in this case, the resulting PEs? It's a super easy way to inject a compromise into a package that will probably get widely distributed.
full disclosure: link is down for me, so haven't read the article. Been a comment that has been building up for a while for me, and not specific to Nuitka. Same goes for new frameworks/languages/etc.