It's not a good idea to have a predetermined "yes" or "no" in your brain for this scenario. It depends on how strong an attack on the dark squares would be -- sometimes it's strong, others it's not as strong. Remember that in order for weak squares to be significant, pieces need to be able to easily take advantage of them. It is dangerous because like you said you are weak on the dark squares, so certainly think twice before doing it! You have to assess how easy it would be for your opponent to attack you -- could he establish his pieces on the h6 and f6 squares quickly? Or would it be awkward for him to maneuver towards them?
If you can survive, then it was a good idea to trade the active bishop for the passive rook, because the passive rook had more potential (ever see a rook in an endgame? For a castle, it's pretty hungry). So you may need to calculate a bit, but at the same time, just see what your hunch is and just go for it! You learn the most that way. The more experienced you are, the better that hunch becomes, and there is no better way to get a feel for the power of the dark squares than getting decimated on them by your opponent!
Sorry for the mixup in the title... Of course, I meant the g7 bishop not the g2 bishop... :)
It's a huge temptation to exchange the dark-square bishop for the a1 rook, but that weakens the dark squares around my king and I'm exchanging an active bishop for a passive rook... Is it really a good idea?