I work for a company owned by Qadiyanis. Is it better that I leave the company to join a Muslim/Christian company? I am an engineer and live in Pakistan.

Praise be to Allah, the Lord of the World; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.

As a rule, it is permissible to work with anybody/company as long as the business is not Haram, even if the owner is not a Muslim. But, it is better for a Muslim to work with Muslims, since they may help him do what is right, warn him to avoid inattention and teach him that which he ignores.
Anyway, if you cannot find work with Muslims, then there is no blame on you to work with Christians or Qadiyanis, although we see it is better to work with the Christians, since you know that they are not, nor claim to be Muslims.
As for Qadiyanis and other deviant sects, it is dangerous to mix or to live with them, since such an attitude may constitute danger to your creed; because they claim Islam and Iman, but in fact they are not.
In reality, it is dangerous for a Muslim to be influenced by them and to be taken from the right to wrong.
Thus, we advise every Muslim to avoid working or living with them unless one's aim is to invite them to Islamic teachings as stated in the Qur'an and the Sunnah. Such a Muslim must be empowered with knowledge that may refute their falsehoods or at least to protect himself.
Allah knows best.