Your SAT will definitely help since it does show you are a capable student and just had one bad semester. Many of the UC’s will ask for a supplemental review where you could send in documentation showing your medical issues for that semester, plus UCB could ask for LOR’s which could also help document this grade drop. The supplementals and LOR’s are by invitation only so if you addressed your medical issues in either one of your personal insight essays or in the additional comments section, there is a chance you will contacted for further explanation.
It really unfortunate that your counselor did not give you the correct information for retaking the courses especially if they were available during the summer. Best of luck and I am sure you will succeed wherever you end up.