I totally feel you on your dilemma. I had similar performance issues (for different reasons) my first semester, which carried over well into this semester, as well. My issues stemmed mainly (so I thought) from a medical condition that adversely affected my performance, but I received some very harsh feedback from my advisor and other faculty. What I eventually came to realize was that I am just not interested in clinical work and the first year of my program is very clinical course-heavy (plus stats). This led to a lot of boredom and lack of motivation, which ended up carrying over into my non-clinical work and strongly affected my quality of life. I got to the point where I was very close to leaving my program because I was so unhappy. However, I took a month or so to mull everything over and I eventually decided to drop the clinical portion of my degree and focus on research only and I couldn't be happier. The faculty at my program was extremely supportive, even the ones who had been my strongest critics only weeks earlier.
Obviously, this is the opposite of the problem you're having, but I still wanted to tell you my story because I learned some valuable things from it. First of all, I learned to be open and honest with the faculty about what is going on. It is REALLY scary at first, but I really found that once you let them know what is going on, they not only view your performance with a different light but they may be able to help you. Don't forget that these people have been doing this for years and have seen countless students go through the same struggles. Maybe ask your professor what the students who "turned things around" did to get themselves on track. Maybe consider taking an incomplete in your course and taking an undergraduate research methods course over the summer to get caught up. Just really take some time to brainstorm how you can improve your situation, or if the situation is worth improving.
Also, as much as your advisor is wanting you to be independent, she is an advisor... she is there to advise you. I have found that professors LOVE when you go to them and admit that you're lost and ask them to help you find your way. Don't feel like they are expecting you to know everything--that is how I felt, completely embarrassed to clue them into how overwhelmed and lost I was feeling. But once I approached them, they were extremely open to helping me through everything.
Sorry, I'm babbling at this point. Anyway, feel free to PM me if you want to talk more!