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.
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.
It goes something like this:
"60% of the UNSC fleet is en-route from other deployments. Estimated time of arrival, 48 hours"
I'd estimate that there are only 36 hours (give or take) between that statement and the departure of the
Autumn. It is possible that a handful of ships were closer, and therefore arrived sooner, engaging the Covenant fleet before the rest could arrive. Also, the
Long Night of Solace may have been an example of one of those "sniper ships" from
The Fall of Reach. It did have a powerful energy projector.