Actually, the Spartan-II's were planetside. There is at least one radio transmission referencing them (check www.halopedian.com). Also, if you place the events of "Pillar of Autumn" during the actual space battle in The Fall of Reach, then there is only one inconsistency left: Autie Dot's (the AI in Reach) information about the reinforcements, as stated after the fourth mission.I have noticed alot of very high brow inconsistencies with canon. Mainly the very instance that Spartan-IIIs were on Reach and not Spartan-IIs who were really the ones fighting the invasion force. Also the Pillar of Autumn was never on the surface of Reach. As for your problem. They may have replaced it due to the fact the plasma rifle has better accuracy at distance and is easier to lug around than a large bulky plasma hellstorm gun. The needler rifle is another weapon i'm rather suprised you didn't bring up but quick comparison to the carbine of halo 2 & 3 show that it was inefficient.
not to mention the ships that chased the pillar of autum were part of the reserve units and only the best soldiers are equiped with the better weapons, since being in the reserve units they probally weren't that experianced there 4 weren't givin very good weapons
Please stop abusing me.