While Penina’s intentions were pure, she did cause Chana major grief. You don’t get rewarded for doing an “aveira lishma” no matter how perfect your intentions are. If you are trying to help someone, but in the process you cause damage to the person you are helping, how much of a help are you really?
Also, we have to remember that Penina was a tzaddeikis, which can easily explain not why she got a punishment, but why the punishment was so harsh.