If you're working somewhere good, this won't be true, or at worst it won't be true after the first year when new employees prove their value. If you're working somewhere bad, then you might see this, but the real problem then is that you work somewhere bad.
Do good work, and work somewhere good, and don't worry about whether the average for MIS is better or worse than CS. Don't worry about averages or what degrees your peers have. Worry about what you make, and what your peers make, and how much value you add vs your peers. I'd take an English major who does builds awesome software oven a mediocre CS major any day, and anyone who wouldn't is an idiot.