She knew what he was capable of better than anyone. She was obviously afraid of him and tired and death was her only way of permanently severing their "connection".
"I say,open this door at once! We're British !"

Maybe she ran out of hope of stopping him.
If we can save humanity, we become the caretakers of the world

i was thinking if she cared so much she could have killed herself early on and saved everyone (though negating the movie)

^^^i was just about to say the same thing. Time wouldn't matter to him.

After a thousand years, Prince Nuada still held a grudge against humanity. Being held captive in a human prison would do nothing to alleviate that. It'd only make him even more bitter and determined to destroy human kind.
Straightedge means I'm better than you.

Hence why I said imprisonment Hellboy could have knocked him out, taken him to a holding facility until such a time, etc - xthe_shiznitx
Yeah, Hellboy
could
have.
However, instead Hellboy did the grade-A stupid move of turning his back on Nuada
again
. Nuala knew her brother nearly killed Hellboy the last time, so she made the impulsive decision that was 100% certain to stop Nuada.
Had she had time to think things through more carefully, she might have come up with a better plan, but time was a luxury she didn't have. And she indicated earlier in the movie that she was at peace with her father's verdict that sentenced both of them to death. In a way she was carrying out her father's verdict.

Hence why I said imprisonment Hellboy could have knocked him out, taken him to a holding facility until such a time, etc
You can't complete your plans if locked up without any helpers to carry out your tasks.

Then they could have imprisoned Nuada until he relaxed enough to stop willingly, she didnt have to kill herself and him. - xthe_shiznitx
The other point is she had to act immediately because Prince Nuada was about to stab Hellboy. Even if Nuala, as the OP suggested, cut off her hand to save Hellboy, Nuada would just get an artificial hand, not unlike Wink, and come back to cause trouble again. As Guillermo del Toro said in his commentary track, Prince Nuada is the idealist in the movie. He wasn't going give up until he achieved his goals. The only way to stop him was to kill him.

Then they could have imprisoned Nuada until he relaxed enough to stop willingly, she didnt have to kill herself and him.

Why didn't Princess Nuala stab herself in the arm? Or if she had to, cut her hand off? She went totally overboard with stabbing herself in the heart. - ronnieronb73
Prince Nuada said it himself, "You have to kill me. You must. Because I will not stop."