Yeah no. None of her missions are suicidal. they are exterminations or investigations of planets/space ships. None of them pit her against invincible enemies.
Heading into the core of an entire planet of Metroids (which, I remind you, are the deadliest things in the known galaxy), alone, without back-up or support, to commit genocide against every last single one of them... doesn't strike you as a "suicide" mission?
Besides, you seem to forget her facing off against the "invincible" SA-X in Fusion, the "invincible" Mother Brain in Super Metroid, and other invincible enemies.
Besides, even then, the Metroids weren't invincible. They were just immune to cold. ... And I was blowing them up with missiles and Power Bombs without Ice Beams long before Other M told me it was "impossible" to freeze them (which, of course, happens only a few seconds after ADAM FREEZES ONE).
Playing a bit of devil's advocate here...isn't Samus basically a gun-for-hire who more or less stumbled into an official Federation op? She really shouldn't exactly have free reign in that kind of situation.
Allow me some fun with a witty and informative counter!
Apparently, the "Federation" op was "off-books" to begin with (they were conducting illegal experimentation), so it was, in reality, not an "official" Federation op. Still, I agree that a marginal compromise should exist so she didn't have free reign... but I draw the line at having someone else limit her own life-saving defense equipment, refusing to trust ANY of her judgement (again, galaxy savior here, boys), and the fact that the "S.O.S." actually came from the scientist division, not the military, and Adam could have easily given her free reign to locate and rescue civilians and lab workers without. It's the same reason we give doctors the freedom to save lives during police shootouts without telling them how to do their jobs. So long as you don't interfere, what would be the issue?
In that respect, it makes sense that the commanding officer would expect her to fall in line if she wanted to stick around, and that she, as a professional, would comply.
At this point, however, I would argue that Samus's legacy and "rank" is beyond Adam's. She's the one who blew up the entire Space Pirate armada, destroyed the Metroid menace, save the galaxy a half-dozen times, and, at least in the Prime games, has the respect and support of some of the Federation's highest ranking officials... folks like Admiral Dane (who, as an admiral, far outranks "Commander" Malkovich). She did what the entire Federation couldn't... on her own.
If Adam was a good Commander, he'd know whom he was dealing with and not let petty personal matters muddy his investigation... but he is petty and those matters do. Rather than let her HELP, he, in actuality, impedes their investigation, limits his assets, and restricts one of their most skilled and brilliant warriors (and detectives, going by prior games investigative puzzles). It was a terrible call.
Samus, even as a professional, would be allowed the leeway to think and act for herself in life-threatening situations. ALL soldiers are allowed the right to refuse cruel or unreasonable orders, and Samus is not a soldier. It's like telling a firefighter not to use oxygen when going into a burning building. Those are just stupid orders.
The screwed up part comes into play when Adam authorizes his men to use weapons that he doesn't authorize Samus to use, the whole Varia Suit thing, and several other instances of screwed upedness.
The basic premise makes a bit of sense, but the execution is bunk.
And, ultimately, it's all in the execution, isn't it?
A good premise can be entirely undone with shoddy execution. I won't argue Other M had some good ideas, but good ideas that don't work in execution ultimately aren't good for anyone.