You can't "suspend" a user from a cohort. They are either a member or not. Likewise, you can't suspend a user in a course if they were enrolled using the cohort method, since the cohort controls their enrollment.
One solution to this issue is to change the user enrollment method for such users in a course from cohort to manual. If they no longer need to belong to the "old" cohort for any other reason, then this will allow them to remain in those courses as usual without any loss of their course activity or grades. You can then suspend them as usual using the manual enrollment method. Swapping them to the manual method gives you the fine grained control if you need to reenable a particular user in a particular course for some reason.
In fact, swapping them to any other enrollment method would allow you to save their course data: just as long as they are continuously enrolled in some active enrollment method. It's okay to be enrolled by two methods at the same time. Don't unenroll them totally and then reenroll them with another method, as data may be lost.
In addition, you could even investigate swapping such users into another cohort that is hidden on the site or is set to be inactive in the course. It would retain their enrollment data but they can't access the course. (The downside of this approach is that you will not be able to enable their enrollment individually since it is still a cohort and you can't control the individual enrollments this way; but that may work for you in this situation.)
Hope this is helpful.