(one and the same)
No, the owl of Minerva accompanies Minerva... It is not the goddess herself.
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.
You have a very difficult time differentiating concepts don't you? She is depicted with her owl, not as her owl... And yes, she was thought to inhabit owls, though those would be common owls, not the owl of Minerva she is depicted with.
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...