The only time Sam stops being so helpful is after she's rescued. Once the bad guys are all dead, Sam passes out so that exhausted, wounded, battle-weary Lara must carry healthy, unharmed Sam down the mountain.
This lack of will, foresight, and intelligence might be okay if Sam was a child or an animal or a helpless person. But Sam is young and fit. Every other friend of Lara's gets a chance to prove themselves and either fight heroically or die honorably. Everyone else can fight, or fix things, or has useful knowledge. At the end, everyone is fighting to save useless Sam except for Sam.
It's not just that Sam seems to be perpetually helpless, she's also an empty shell of a person. Her life revolves around Lara, and the only thing she ever talks about is how awesome Lara is and how wonderful it is to be with her. She doesn't seem to have much else going on in her life. Her reason for taking the voyage in the first place is because she's the only one who believes that Lara is right about a certain theory. Sam even wants to make a documentary about Lara. Even Sam's connection to the story - the whole reason the bad guy wants to sacrifice her - is the result of her bloodline and not related to anything she's done. Sam is completely passive and life just happens to her.
Over the years a lot of people have complained about this "Damsel in Distress" idea. This is particularly true of women, who jump into a game hoping for a fun power fantasy and too often find the only woman in the game is some helpless bimbo with no sense of ingenuity or initiative. After a while this can really start to grate and eventually we find ourselves arguing about how sexist a character trope is. Some people will defend this game by pointing out that the ultimate badass of the story is Lara, with the idea being that it's okay for Sam to be stupid and weak because Lara is resourceful and strong.
But before we unleash the kraken of gender politics, it's important to remember that Samantha's problem isn't that she's a weak woman. Samantha's problem is that she is a horrible character. She only exists to stroke the protagonist's ego between rescues. She has no important dialog, she needs to have everything explained to her, she doesn't get any funny lines, and despite being in almost constant peril she doesn't seem to go through any kind of character arc. She's shallow, she's annoying, and the story would be better if she was just replaced with an inanimate object for the two sides to fight over.
Yes, far too many times the inept doormat character that we have to rescue ends up being a woman. But making Samantha into Samuel and having Lara rescue a spineless whiny dude wouldn't fix the problem that the person we're trying to save is the least interesting person in the game. Let's not argue over how sexist this character is. Let's get rid of it and replace it with something better.
To fix Samantha, just give her some strength, skill, and determination. It's okay if our rescue buddy can't liberate themselves. I don't begrudge a character not being able to free himself or herself from an army of cultists. Just show that they're trying. Make them good at something besides fighting. Make them a character with thoughts of their own. If nothing else, give them some witty things to say. We don't need to enact some kind of perverse affirmative action quota where we make sure both genders are properly represented among terrible sidekicks. Let's stop having terrible sidekicks.