(one and the same)
I hate to rain on your parade, but the greek goddess and the owl are one in the same, it's called zoological idol transference. The greeks had gods for everything. They thought their God's inhabited certain things. Such as - Zeuss - the heavens(clouds).
The spirit of minerva was thought to inhabit owls.
The spirit of minerva was thought to inhabit owls.
Either way the transference you're talking of isn't exactly relevant to the discussion. Minerva Mcgonagal in Harry Potter was in fact named after the Goddess Minerva. Of that there is no dispute. The owl of Minerva has nothing really to do with this.
Back to the point, being named after Minerva doesn't make the thing evil, many people are directly or indirectly named after gods and goddesses of myths...