After an earlier incident I decided not to do good mornings ever again. Don't bother trying to convince me otherwise. I know this makes Wendler furious, but I don't give a shit, I like his program so I'm doing it anyways.
Yes, if there's one thing Wendler talks about nonstop, it's that the assistance work should always be followed exactly as he wrote it and people should never ever customize it according to their health, abilities, and goals.
What are you trying to achieve by doing them - low back strength? Glute/hamstring strength? Low back size? Glute/hamstring size? Different tools will do different jobs.
What days are you putting them on, what does the rest of that day look like, and what's the rest of your training week look like (days, exercises, sets, and reps)?
I used to love having clients do this exact thing when I worked in a regular gym (without access to a reverse hyper machine). Holding the pause at the top for a full one or two-count gives it a little extra something, since you often end up dealing with a little "bounce" from the Swiss ball.
They don't really lend themselves to added load though. Holding a DB in the feet would be the only option (which can be awkward in the bottom position), but I rarely found it necessary with moderate-to-higher reps and that pause at the top.