If someone brought in a $50 part that required you to pull the engine for replacement, I don't think you'd mind just charging labour. If however someone brought in a $2500 BBK from a company that you were an authorized dealer for, I can see how you'd be pissed.
I'd say raise your labour rates, and give a "discount" to customers who buy their parts from you. A "surcharge" would ruffle feathers, while being denied a discount would be seen as the price to be paid for bringing their own parts. No one could fault you for that. Perception is the key.
Koz.

2001 A6/4.2 Sport/Premium/Guidance.