I guess she also may not want weed in the house because she knows she can't help herself...
It is wrong of her to steal from you and she needs to learn some self restraint.
On the other hand, it is her apartment and you're kind of rubbing her nose in your habit.
I think it'd just be better for you not to smoke in the house or not take back such large quantities, or just keep your weed on your person in smaller amounts. I know people are going to call me a nutcase but I always have my weed on me in case my dad decides to 'investigate' my room again.
Okay, maybe don't do that and get caught or it'll be on my conscience forever -_-;
Get one of those mini safes for cheap when you're out of the house for your own peace of mind even after confronting her. Regardless of what it is she shouldn't steal from you.
Even runnig outside to smoke? Or smoke out of your window. I've done it for the last 3 years.