Indy's brother said:
I also think that through his experiences with the villains of the OT, there was little point in trying to talk Spalko out of it. And why should he? He didn't warn Belloq. He didn't warn Donovan. He sure as hell didn't care what happened to Mola Ram. He tried to save Elsa because he had seen a human side of her and was emotionally and physically involved with her at one point. Not so with Irina. Spalko ordered her men to gun down U.S. Army soldiers. On american soil. I think that Indy would have little sympathy for her.
The murder of the US guards was on Colonel Dovchenko's orders. He was the Soviet Special Forces officer in charge of operations on this mission.
Colonel Doctor Spalko was KGB, from a psy-ops investigation department. On this mission she's an intelligence officer. While the duties of command are shared, she might wash her hands of Dovchenko's choice of action.
For all her threats to kill Indy, she knew that she was better off with him alive and helping her.
The Lucasian motif for seeing good in compromised characters (i.e. Anakin/Vader) resurfaces in the Indy films. We see it in Indy himself throughout, where he justifies his actions by the end result. Occasionally he just conforms to the standards of the day (e.g. looting artifacts from sacred sites).
The Temple of Doom saw Indy at his most selfish point, but the good in him was drawn to the surface by chance.
Belloq and Toht had no mitigating circumstances. Toht was purely sadistic, and Belloq purely ambitious. Dietrich was in too deep, and the mission commander reporting directly to Hitler. He also ordered Marion thrown into the Well of Souls. There could be no saving these three, as none of them showed remorse.
Mola Ram, Donovan and Vogel were all highly ambitious, and visibly enjoying their moments of power. Mola's evil is all too obvious, Donovan shot Henry Sr to force Indy to do his bidding, and Vogel was another Nazi sadist.
Indy didn't, or couldn't, do anything to save any of these characters. They wouldn't have been worth the effort in terms of society.
Although Indy was personally involved with Elsa, she was also only associated with evil by ambition. She was
using the Nazi Party to get what she wanted. Her actions in the end wouldn't have supported the Party, as I think she planned to escape with the grail. Hence Indy sees something redeemable in her, something worth trying to save. It could be argued she was possessed and not in control. Though if she survived, her sense of loss might commit her to a life in some grim asylum.
I see Irina Spalko as somewhere between Elsa and the others. High ambition leads her to commit unsavoury actions. As far as she's concerned the Soviet Union is at war with America and other western countries. Albeit an undeclared Cold War. Some fairly nasty things were being done (and would be done) undercover on both sides of Churchill's 'Iron Curtain'. Think of the CIA's actions in Cuba.
Like Dietrich, Spalko is doing her duty in the name of her country - or in both their cases, in the name of the Party, since both were given their missions by the Party leader. That makes her compromised, and she would have been further compromised if a key character scene hadn't been deleted: the telepathic experiment in which she killed young rabbit's one by one to test their mother's reactions.
There was some kind of connection between Spalko and Indy right from their first meeting on screen. She had respect for him, though it was measured and tempered by her duty to the mission in hand. It was in her interests to keep him alive, professionally and maybe personally.
In return Indy would see in her traits of Elsa's character. Spalko was possessed by her need to find what lay at Akator.
In the moments before her demise:
SPALKO (cont’d)
Imagine what they’ll tell us.
INDY
I can’t imagine.
(she turns, looks at him)
Neither could the humans who built this temple, and neither can you.
SPALKO
Belief, Dr. Jones, is a gift you have yet to receive. My sympathies.
INDY
Oh, I believe, sister. That’s why I’m down here.
...
INDY (cont’d)
--it wants to give us a gift.
The Being seems to look right back at him. Spalko moves closer to the altar.
INDY (cont’d)
A big gift.
Spalko is speaking to the figure on the altar, low, fervent, almost a prayer.
SPALKO
Tell me-- everything you know, I want it all, I want to know --
Indy does try to warn her, in stating that she "can't imagine" what the aliens will tell her. There's that line Indy won't cross in dealing with the supernatural, but he knows it's far too late to prevent Spalko from continuing. Her life has been building up to this event.
She had been the prime threat to the alien's mission to leave Akator, and the aliens show they don't have a passion for mercy. They punish her without holding back, and without sympathy for the capacity of the human mind.
Spalko was a redeemable character, but she, like Elsa, made it impossible for Indy to save her. The aliens delivered their form of justice, and those that survived would carry that message away with them.