From an RP standpoint: Yes, since there is no expression for enemies to attempt to capture you in the game, killing on sight is a reasonable action. Moreover, it's clear while Malak preferred to take her alive, he wasn't that concerned about it given he ordered the entire planet destroyed just to remove her as a factor once it became obvious he wouldn't find her.
An easy solution would have been to just have a quest in the game that allowed you to find a disguise for her, but I guess Bioware never thought of it. It's amusing though that for some reason they made a huge deal of her being recognized on Korriban, but not on Taris, despite all of the Sith actively looking for her there. Lol.
As an aside though, it doesn't make sense for any of your Force Sensitive party members to be allowed on Korriban, since Uthar or Yuthura would pick up on their sensitivity immediately and the jig would be up.