Between your MCAT success and doing well in graduate-level courses it looks like you have proven your ability to handle difficult science classes.
It will all come down to how you explain your poor early ugrad performance, and more importantly what you've learned and how you've grown.
It all depends on your ECs, letters of rec, essays, and interviews, but if you apply broadly I think you actually have a decent shot. That MCAT may just be your saving grace.