I'd argue that he proved he can do the work if he took two semesters full of upper level bios. A lot of Med schools are now just three semesters of tough science coursework (depending on the definition of tough i guess lol)
OP, I would maybe wait a year to apply (so dont submit this year, but 2018) and round out the resume with working full time in something clinical and meaningful, while also taking at least one more course fall 2017 and another course in spring 2018. Show the adcoms you can commit to working 40 hours a week with work and also do well in another tough science course. Clinical experiene goes a long way in making yourself stand out as an applicant, and also maturing you as a person.
Don't get your hope set on any particular SUNY. The application process is a lottery. You just gotta give yourself the best odds you can. FWIW, I got in with under 3.4, and 30 MCAT, but had almost 6 years of meaningful clinical experience work. the work experience went a long way