Most pharm schools do not care when or where you take your pre-reqs, as long as you get them done. Yes it's not good to get a whole semester of Fs, but doing well when you retake those classes and doing well in the rest of your classes should get you into pharm schools. You can also typically explain why you had a semester of bad grades, so you can help yourself out there. I think you should do whatever you can feasibly do and are comfortable with. Start pursuing the different avenues and see what is the best option for you.