I wouldn't have thought so, as a pen is more permanent, so if anything would only be confirming the appointment even more than 'penciling' someone in would be.
For example, the person says "Should I pencil you in?" and you could say "No, I'm going to be there for sure! You can pen me in!" But it's not a standard idiom; you would just be playing with words.
The expression 'to ink in' can be used in this sort of context:
"OK, you'll be here tomorrow at 12.00. That's definite is it? You're not going to change your mind again. Can I ink it in?' (It's pretty informal, but I've heard it used - in the UK that is.)