It was hard to tell which side she was on. She kept Indy alive when Standardtenfhrer Vogel (He was SS, and that's the rank for Colonel) wanted to kill him and his father. And when she takes the book from him in front of Vogel, it was probably best that she didn't do anything to help Indy at that point.
I think that she was on the side of the grail, and whoever was going to get it for her. When Indy was rescuing his dad, and those soldiers busted in, how did they know that he had the book? So Elsa had to have been in on it. Then later on in Hatay, she tells Donovan that they have no time to lose because Indy and his father have escaped.

She was banging hot.
Now in the fourth film had he left Marion to die, that i would have understood.
i told you not to stop, now lets go - Apocalypse Now

Elsa did just say that she would share the Grail with Indy. I'm guessing he interpreted her as implying she'd marry him. That would be a strong motivation for saving her.
He did seem to have genuine affection for her. Trying to save her, calling her "honey" and being clearly sad after her death.

She was hot. Just for that shallow reason alone I'd have tried to save her.

But it was rather wonderful
http://amessagefromdonaldtrump.ytmnd.com

She was a back stabbing harlot.
Brony who is also a Metallica and Iron Maiden fan.

But she was hot.
Seriously though, she did betray her Nazi co-worker to save Indy and Henry. I think she could be redeemed.