Resigning isn't a killer for getting on with most companies. There are numerous reasons why people resign...new opportunities, family health issues, moving to take care of elderly parents.
Most savvy HR reps will tell you that due to HIPAA and other restrictions they can't really delve into why you resigned. If you had been fired for cause or terminated, that's a different issue.
However, your employer obviously didn't want to torpedo your future career so they gave you the option of resigning.
I wouldn't worry about it if I were you.