As long as you have a very good reason for not being able to live together, and you can prove your ongoing relationship while you are in Geneva, it shouldn't be a problem.
Though, is the internship voluntary/will it further your career, or is it something you are applying for because you fancy it? Normally acceptable reasons for living apart during a spousal visa are things that are out of your control - such as one of you being sent overseas/on detachment to another city by your employer, or being deployed overseas with the military.