Internet Kraken said:
Wait, there really wasn't any justification for killing the metroids in the second game? I kind of assumed there was. Weird. Still, thinking that this has any reflection upon our treatment of other species in real life is pretty silly.
There's the explanation that Metroids are dangerous and difficult to kill parasites that the Space Pirates intend to use as biological weapons (a concept more thoroughly explored in
Metroid Prime). Of course, the Federation's desire to study Metroids allows the Space Pirates to revive the species from extinction and continue their plan of using them as biological weapons.
Similarly Samus destroys the research station in
Metroid Fusion while causing massive environmental damage to SR388 (Metroid and X homeworld) to prevent the Federation from attempting to use X parasites as biological weapons. She reasons that X are far too powerful and adaptive for Federation scientists to control, thus the X will escape and begin their Tyranid/Zerg/Flood-esque campaign for universal proliferation. Essentially she's causing genocide to prevent a greater genocide.
On to
Metroid Prime 2: Echoes: the Ing's ability to possess beings in the "Light World" would afford them the capability of interplanetary travel should they gain control of functional starships. This coupled with their extremely hostile nature and the incredible difficulty associated with fighting them is a credible reason for their destruction.
Same thing with the destruction of the lifeform Phazon, which was finally achieved in
Metroid Prime 3: Corruption. Phazon leviathans had been wreaking havoc on many worlds, and the Federation saw no option besides the destruction of Phaaze to stop it.
All of these things are comparable to wiping out small-pox. In all cases really these organisms are far more threatening to civilization than any possible Earth creature that we can conceive of save for highly communicable, highly lethal illness causing vectors.
As for Samus' wanton slaughter of local wildlife in her missions? Well, they're aggressive and/or in the way. If soldiers were attacked by wild wolves while on a mission would you say that they're supporting genocide by killing the wolves? Well now imagine that they're being attacked by massive snails with spiny shells than can cut through metal, or horse-sized grasshoppers that can launch spike projectiles at dangerous velocity.
EDIT: FYI, this isn't necessarily taking your OP seriously. Rather it's further over-analyzing the series to come up with the moral justifications for all the issues that the initial over-analysis raised. Interesting thought exercise.