Supplication against the Oppressive Yahood is permissible, but we must also….
Shaikh Saaleh Al Fawzaan (may Allaah preserve him) stated:
The actions, disbelief and evil of the Yahood is well known, even (with regards) to (their relationship) with their Prophets. They killed their Prophets and (also) is that which occurred with Kaleemullaah- Moosaa (alayhis-salaam), such as what Allaah has related in the Qur’aan (regarding) the story of Moosaa and Haaroon (alayhimas-salaam).
The character, disbelief, misguidance and evil of the Yahood is well known, even towards their Prophets; but what is obligatory upon us (Muslims) is that we ponder and rectify our deviated affairs and repent to Allaah; because the Yahood have not gained the upper hand over us except due to our sins. Why is it that we do not hear anyone addressing and admonishing the Muslims whilst saying to them: What has happened to you is (nothing else), but as a result of your turning away from the religion of Allaah and negligence in the affairs of the Deen. So repent to Allaah in order that Allaah may aid you and avert the plot of the plotters from you.
We do not hear except insult, abuse and supplication against the Yahood, but this should be substituted with supplicating to Allaah to rectify the Muslims and to make them steadfast. And to mention to the Muslims that they should repent and return to Allaah, and rectify their Deen for the sake of Allaah. This is the first obligation.
As for supplication against an oppressor-be it the Yahood or other than them, then there is nothing wrong with this. It is legislated to supplicate against the one who oppress you with the sharee’ah supplications-the supplications found in the Book and the Sunnah. But before supplicating against them, you should supplicate to Allaah to rectify the Muslims and to make the Muslims steadfast upon their Religion and return them to the truth. (And) advise, address and admonish (them) with regards to (obedience to) Allaah. This is what is obligatory.
[Source: Al-Ijaabaatul Muhimmah Fil Mashaakil Al-Mulimmah (page: 202)