While a non-issue if you have more than a single AFMU, B-class AFMU's have higher integrity than other grades, which means that they handle heat damage better. However, as I found out with some testing, Supercruise collisions don't care about module integrity, so whether you have a D-class, B-class or A-class they all seem to take roughly the same damage during collisions (SC collision threshold I think is 200km/sec).
I equip B-class AFMU's on all of my exploration/general purpose ships and then use the "Shielded" mod to further boost integrity (This uses +80% more power for G4 Shielded, so power priorities must be set and the AFMU disabled until required). A good part of this is due to the higher integrity, but another part is keeping costs down (regardless of how much cash I have, I can't deal with how overpriced some of the A-class modules are compared to B-class

).
I can see though that A-class AFMU's will get your FSD repaired quicker, so if you are looking to cover distance quickly using Neutron star boosting, this would be a good case for it; and if you have more than 1 AFMU, the B-class loses any advantages it had over A-class (apart from the price of course

).