How do you manage your career at a bad company?

 MT fanatics,

How do you manage a career for success in an organization with a horrible reputation? How much of an organization's reputation plays into a job search?

Background:
I work for a Pharmacy College as a Resident (1 year contract). This college's leadership has backwards thinking. They don't listen to solutions to major problems. 
Local organizations and pharmacies all over the area know of this school's reputation. Students who graduate are bottom tier. 

My residency is only for a year. I hope to search for a job in Michigan, which is far away from my current employment. 

I work hard now. I lead and create projects not assigned to me. I deliver results. My few performance reviews are great. I continue to improve on my weaknesses. I hope to deliver enough results to impress recruiters. 

I am afraid that as I interview soon for positions elsewhere, recruiters will see my college's name and put my CV in the trash. 

Any guidance is greatly appreciated

Alex