Jeremy,
The gutter covers the splice line between the roof panel and the wall. If you remove the gutter, you will have to fiberglass the open seam that the gutter covers. A seam this long is very difficult to glass-in without it forming cracks as you drive, So even though the gutter is technically not structural, you do not want to remove it. The rubber filler strip is for appearance only, and serves no other purpose.
Gerald