>>731178580's & 90's dolls can go through the zit creme procedure just fine. It's 50's & 60's dolls that you have to be careful with.
However, the zit creme procedure does not work on standard Barbie bodies. The zit creme works on soft, vinyl plastics, like the ones used in hollow baby dolls and Barbie heads. Barbie bodies & most action figures use PVC/ABS hard plastic.
To clean the mark off your Barbie's neck, I'd recommend grabbing some GOO-GONE at your local store. It's cheap and takes lots of difficult to remove marks off. Just apply the goo-gone to the mark, let it sit for 5~10 minutes, then wipe away the mark. It should have no problems removing sharpie marks from the body. Just becareful not to apply the goo-gone heavily on any painted surfaces, like the Barbie's eye paint, as the goo-gone will remove top coats of paint if you're not careful.
Hope this helps. I didn't want you to go get some zit creme and find that it doesn't work on hard plastic marks.