Considering the spread of infection in Florida right now, I would absolutely not put a CM in the unfortunate position of disappointing a little girl by refusing to touch a guest's pen. That said, I think this is a great opportunity to do something fun and new (though along a similar line to your customary tradition) .
What about getting a box of large alphabet flash cards (which should be no less cumbersome to tote around than an autograph book) and do an "A-B-C of Disney" (or "A-B-C of Vacation") photo book? Your mission would be to accumulate 26 photos over the course of your visit, one for each of the letters in the alphabet. Take a photo of your granddaughter holding up the corresponding card for each of the photo subjects and put the pictures all together, chronologically, in a photo book after your trip (I highly recommend Picaboo....they are easy to put together, the finished product is LOVELY, there are various size options for the books, and there is ALWAYS a deep discount available on Groupon).
So, you could have a photo of her at the airport for "A". Riding Splash Mountain for "S". Eating a Zebra Dome for "Z". Or, if you want to focus on a specific theme, go for all food pics (with a giant bag of cotton candy for "C", a popcorn bucket for "P", etc.) or even people (perhaps you could get a photo of her in front of the balloon CM for "B", a picture in front of the Walt statue at MK for "W", with a lifeguard in the background for "L", with a personable Photopass photographer for "P", etc.). I am sure, as long as she remains 6 feet apart from the CM's, many would love to pose for a photo as long as she stays in the foreground and they are in the background......and how fun would it be to get, say, a pic with the ferry and a ferryboat captain behind her?
If your vacation is dwindling down and you still have a few letters you haven't been able to find, I bet Guest Services would have some spectacular ideas for you if you drop in and tell them what you're trying to accomplish. And you could always plan ahead on a few of the trickier letters by posting here on the Dis for ideas before you leave.
Hunting for characters has been one of our favorite things to do on our trips, so that aspect will be sorely lacking this fall (assuming our fall trip actually happens.....with the state of things lately, I'm no longer holding my breath). I'm even considering of doing something similar to this on our own trip this year, especially with Food & Wine (I'm thinking the ABC's of Orlando - Food Edition might be quite a fun challenge!). In the end, your granddaughter would have a fabulous souvenir and I bet she'd come up with some amazing ideas for each of the letters.......kids think entirely differently than adults, and her creativity might make for some spectacular moments!
I'm not sure of your budget, but if you were looking for some splurge opportunities, this would be a cool way to incorporate them. Instead of A for airport, what about A for an amphicar ride at Disney Springs? (assuming they have reopened, I honestly haven't checked) Or, enjoy a ride on the Characters in Flight balloon (for "B") or a round of mini golf (for "G" or "M").