This may vary dramatically from school to school. As long as you take the summer class at a school with comparable rigor to your usual university, you will be just fine.
It's quite common at my undergrad school for people to take classes over the summer, and many of them do very well in medical school admissions. Maybe SUNY Upstate cares about this but I haven't heard it to be the norm in medical admissions to weight summer classes so negatively.