Oh, there were a LOT of people expecting Penny to show up this volume in some form. At the same time, almost no one expected it to be in episode one, and more importantly, pretty much everyone I've seen that thought of the idea was expecting it to be a lot more painful from the word go. That it would look and sound like Penny, but it was clearly a new intelligence and soul inside, potentially even one hostile to RWBY and JNPR outright. That fear died the moment Penny saw Ruby, and the S.S. Nuts N' Dolts set sail again
(It also helps that shot of her in the opening is so very 'Anime Love Interest Shot')
At the same time though, there's still a lot to worry about. Not only is Watts still out there, with all his potential hooks into the Atlas systems and possibly Penny, there's the question of how she'll react to JNR in particular, and just what trauma does linger. There's a price to be paid for a resurrection like this, and learning it will almost certainly hurt. That said, I'm expecting her to survive. Killing her a second time is too cheap.
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Spoiler