In a fanfiction I´m working on, there even is a somewhat logical reason for Penny to still be alive in the actual show. It´s based on a theory according to which Penny meeting Ruby had some effects on her programming.

The short version is that various random lines of code began popping up, mostly due to Penny´s cybernetic brain developing at an much higher rate than what it was built for. When Penny was hit by Pyrrha´s semblance, the powerful electro-magnetic shock caused these lines of code to clump together and form a new program, which served only one purpose: Self-preservation.

When Penny realized that she wouldn´t be able to survive this impact, her new program transferred her entire mind to another place, so it could be saved. This place, of course, was Ruby´s scroll.

Now, I know the biggest problem here: If Penny has been on Ruby´s scroll the entire time, why didn´t she say something? Easy: She couldn´t. I mean, we´re talking about a human brain, in terms of processing power, being uploaded onto a scroll. That´s like putting the entire iTunes store on a single cellphone.

However, now that Ruby is in Mistral, and close enough to the CCTS Tower of Haven Academy, it might be possible for Penny to upload her consciousness onto the tower´s computers and leave her dormant state on Ruby´s scroll.

Also, I like to think that Qrow would ask her to hack every single scroll nearby and search for any mentionings of the name Salem, but that´s just an idea of mine.