Well, this is one of those situations where you need to figure out what your boundaries are. So, if your goal is to make her happy, then if tokin' weed makes her happy, you gotta go with it. As you say, you realize she is her own person, so if she is going to choose to toke, you'll need to be your own person and decide if this is an issue you can live with.and if you can't handle it, then its a matter of where are your priorities? Maybe it could be time for a break to see whats more important for both of you. The 6 month mark in a relationship is generally that point when all the rainbows and hearts and flowers starry eyed sugar stuff is waning, and mutual respect is waxing (if a relationship is going to make it long term, that is). Examine yourself and figure out why you are dead set against the weed. From that point on, it's a matter of personal boundaries, and if she wants to smoke weed, and you've already made your position clear then making her quit for you will only create resentments down the road as she'll feel its manipulation and control by you. If you try to look past it, especially if this was agreed upon from Jump Street, then she went back to it, you'll resent that fact too, and by the way, understandably.
Just to let you know, I've been tokin' since the early '70's. A few years back, DH stopped for job purposes, but I still like to get a buzz. For us it's just a matter of individual preference, and it doesn't make a difference as far as our relationship goes, but that's us. We were already together for 20 years before it became a matter of she does, he doesn't.
As you are still in college, and things are very different now than they were in the '70's. In today's job market, her tokin' could severely limit her job prospects. Back in the day, companies that hired were'nt interested in what you did on your own time, but in today's job market prospective hires are generally expected to pass drug tests. These are all considerations that are important, and your future could literally go up in smoke...and if you throw in someone getting busted and having a record for a narcotics charge, that can screw your future job prospects too.
Time for an honest discussion between you, examine your individual priorities and if hard decisions need to be made, then now is the time to make them. You are both very young, so you want, and need to experience life. You'll either accept it and move on together, or it could be one of those deal breakers and if so, then you just have to move on.