I imagine she looked at those shakers and thought, "They're so little that they don't need a box. Look! They fit right in this envelope!"...which goes to show once again that common-senselessness is rampant.
No, you were not wrong to ask the seller to ship your replacement in a box. But I hope you did it nicely. Not that you shouldn't have been ticked off - but smiling communicates much better than yelling. I haven't been selling much on eBay lately, but when I do I always seem to listen better to buyers who don't treat me like the idiot I already know I am.
I probably would have said, "Yes, I'd appreciate a replacement. It will be more likely to arrive here safely if you wrap it up securely in bubble wrap instead of tissue, and put it in a box rather than a bag. I know it's a little more trouble, but I think you'll be surprised at how much better the Post Office will do with your products."
If she shrugged off that sound advice and shipped the replacement in a bag anyhow, I wouldn't do business with her again.