Not sure what seal you are referring to, but I would guess it's the accordion-like ones that flank either side of the moonroof. Generally, you can gently press them back in place, but if they have indeed torn, then yeah, they need to be replaced.
The only thing that ever gave me an issue was the spring-loaded metal wind deflector assembly...one of the guide rods broke at the fastening point. MB only sells the whole assembly ($70). About a 15 minute task to replace.
To reduce wind noise almost entirely, purchase an aftermarket plexiglass wind deflector. Even with the top fully open, you can carry on a normal conversation in the cockpit!
