Well, of course if you want to study specifically the band gap and some impurity levels, then it's fine to use the approach you mentioned. The molecule also breaks the periodicity, so you get a new Brillouin zone, if you wish. In this case the zone folding just means you get more bands, but it doesn't affect the gap.
You just have to be aware that you cannot directly compare the bands to those of the single unit cell of the ribbon. However, in any case you had better look at the density of states more, perhaps, than the band structure.