I'd agree that it has a lot more to do with the school culture than a general across the board distinction between the two types of schools.
I have worked in 6-8 schools, as well as k-12 schools and the way 6th graders are treated is entirely dependent on how the oldest students treat younger ones, and the attitude fostered by the teachers and administration.
If there is an atmosphere of older classes doing projects with younger ones, or being paired as "buddies" for certain things then the cross age bullying is drastically reduced since the older kids see the younger ones then as their friends and "little buddies" as opposed to easy prey.
Some younger students like the way a 6-8 school treats them as more of an adult, but with the warm fuzzy side of elementary when needed while others would prefer to drop the warm fuzzy elementary feel to some middle schools and jump right into the high school feel of a school. And still others like the security of being the older students in an elementary they are familiar with that still gives them the warm fuzzies typically associated with younger grades.
I'd investigate the cross grade interactions (both scheduled - like mixed pe classes, and class buddies, and random - like mixing in the hallways or membership in an activity) at both types of schools before making a decision.
