If you get accepted into the molecular biology program, but this is not your first choice,
will you be able to change/switch programs (in third year)?

Yes of course, but you need a certain gpa to switch. I think its around a 9.5.

Best of luck!

You don't need a 9.5 average, it depends on the program you want to switch into. For limited enrollment programs it also depends on how much space there is.