My personal opinion is that the Rare Blood division will be better off long term. The product is great, however, incredibly rare. You might be lucky to get 1 patient that year. As long as you can be prepared to stay motivated without having anything to show for it (common in rare disease), and know that field can take years to build up, you will be alright. Both divisions will let you be marketable elsewhere, but I think rare gives you an extra advantage for the future. More and more companies are launching orphan drugs, and they want people with that experience.
I cannot tell you the pay for either division, but know that Sanofi does pay one of the lowest out of all the other pharmas/biotechs. But if you are breaking into one of these divisions, it's worthwhile getting the experience, and leaving for higher pay. Sanofi hasn't learned from that yet. Then they wonder why everyone is leaving for other biotechs/orphan drugs.
Good luck to you.