People don't seem to understand that said scene made sense in many ways. Other M is the game that takes place after Super Metroid, and in this game, Ridley is killed by Samus.
Ridley is also "killed" by Samus in the first Metroid, he straight-up disintegrates. Then again in the first Prime, where he falls into the Impact Crater while being shot by like six lasers, then explodes. He is "killed for good" again in Prime 3, where Samus watches him melt into ooze right in front of him. Then again in Super Metroid, where he, again, falls apart like he was made of paper mache.
It didn't make sense. Samus has "permanently killed" Ridley in every game he's appeared in. Never once has he just flown off. She should be expecting him to come back at this point, and it makes no sense that this random time of him returning made her lose her ****. It wasn't good writing, it wasn't an emotional moment, it was just Sakamoto trying to elicit an emotional reaction from an audience by giving Samus some out of character reaction to her main nemesis, without explaining what made this particular instance any different from the last six times he'd come back from the dead.
Sums up the whole "characterization" thing.
Just because we see Samus freeze up over Ridley in Other M prior to the fight doesn't mean her "character" was butchered. She still beats him half to death.
Say Mario, out of nowhere, freaks out when Bowser kidnaps the Princess in the next Mario. He has a serious mental breakdown because of it, even though it has literally happened a million times.
Shigeru (Sakamoto) then says, "This is the Mario we wanted all along! You know that happy-go-lucky, unstoppable plumber you've known and loved for so long? He's actually just a sniveling crybaby, and that's how he was supposed to be all along!". Mario, of course, still stops Bowser because that's how games work.
The same exact thing happened to Samus, and it pisses me off. The entire game took a huge **** on an already-established character because "Samus didn't have a voice, which means she has no personality", which is bull****. Retro did a better job of portraying Samus within the last ten minutes of Prime 2 than Other M did for the entire game.