Is there any real evidence that the Shivans tried to exterminate the entire crew, though? From what I gather, Bosch and his top lieutenants were waiting for the Shivans. Then either the Shivans barged in, or they talked with Bosch, but end result was that the marines died, Bosch was taken, and a bunch of Shivans were left behind.
I think there was one transport that was leaving the Iceni that you could destroy...so maybe two, three transports full of Shivans?
Going by Bosch's predisposition towards meeting the Shivans, he might not've had guards with him at the time. However, I'd guess that the airlock would be the most guarded area of the ship, especially with Shivans docking. Past that area, though, they could probably wreak havok pretty much unmolested. When the guy on the bridge said that thousands were dead, Shivans too, he may have been exaggerating a little. But any Shivan deaths would be major events.
So, I don't think handheld weaponry would have to be a lot better - just the tactics. One guywith a grenade launcher can probably take out one Shivan; if marines started stocking up on those, kill ratio of shivans to humans would rapidly get better.