James was the deleter. KG was the one dumped in the lava. That's why he's MIA, nobody saw him die except the one who killed him, and he would not report that for obvious reasons.

There were no ice-resistant Metroids? It doesn't really add up for them to exist; Samus still got the ice weakness in Fusion, and all of the Metroids you see are still weak to ice, except the Queen, who resisted ice back in Metroid 2 anyway, and she still takes damage from the ice beam when you shoot her in the gut with it. My guess was that MB intended to lure Samus into sector zero, then eject it into space; Adam made up the ice Metroids to convince Samus not to go in. That one dead creature in sector 2 could've just been by a higher-stage Metroid, considering that none of the higher-level Metroids in Metroid 2 took any damage from ice; the Omega Metroid in Fusion was presumably because the plasma+ice mix, since it didn't take any damage from ice missiles.

If there are ice-resistant Metroids, she wouldn't eject sector 0, that's correct. The issue is, the only evidence that there were ever ice-resistant Metroids is that Adam said so, based on the highly-compelling reason that "It's hard to imagine the military mass-producing defective weapons". He's very clearly not omniscient, considering he still acted like MB was in that sector and couldn't explain why the baby Metroid was very much not ice-resistant. Well, and also the part where he said that Madeline Bergman was not your ally, and then sent you off to find... Madeline Bergman. Erm.

Samus mentioned during Madeline's speech that there was a project to create ice-resistant Metroids, yes. The only products you see of this are a perfectly normal queen and a dead creature in sector 2. Considering higher forms of Metroids seem to resist ice anyway (see: Metroid 2, where Omega Metroids are immune to ice beam, and Metroid Fusion, where the Omega is damaged by ice + plasma but is still immune to ice missiles), it's not impossible that was done in a different way. For that matter, if you treat Prime (US version) as canonical (one or two lines of dialogue suggest Prime 3 was not included), there was a (Hunter) Metroid living in Phendrana, and Fission Metroids could end up immune to ice (and yet nevertheless ended up rather severely dead).

Even if Samus could survive space, if she was separated from the ship by a significant distance, there was precisely nothing she could do before the feds got clobbered, just considering their track record with even regular Metroids. The phrase "not heard from again" shows up with distressing regularity.