There's a third meaning according to
https://en.wiktionary.org/wiki/sigil#Noun which will be familiar to perl programmers - $var vs @var vs %var.
I don't know which meaning the Sigil author had in mind. There are risks to using the "magical" definition because that will deeply offend some people. Perhaps the seal/signature/signet definition is "right" because of the way Sigil rewrites epub files in a clean way.
It still doesn't really say "ePub editor" to me, nor does it even say "does something with ebooks".
The fat white border version of the logo reminds me of the Skype logo.