Praise be to Allah, prayer and peace be upon the Messenger of Allah, Prophet Muhammad and upon all his Family and Companions.
Islam has spared no effort in protecting civilians and guarding vulnerable women, children, elderly people and monks against the scourge of war. This is reflected in Prophet Muhammad`s order to His army as authenticated from Anas (May Allah be pleased with him) who reported that the Messenger of Allah (PBUH) said: "Go in the name of Allah, and His religion and that of His Prophet`s. Look! Don not kill an elderly, a child or a woman. Do not hide war spoils, but gather them in one place. Adjust the matter of your difference and be virtuous for Allah loves the virtuous." [Abu-Dawood].
This was also the directive of the Prophet`s successors e.g. Al- Bayhaqi narrated that Abu Bakr (may Allah Be Pleased with him) said to the soldiers sent to Sham (Syria): "Look! I advise you to fear Allah. Be not dishonest. Do not deceive anyone. Do not hide the spoils of war. Do not kill the aged, the children and the women. Do not set fire to date palms. Do not cut down fruit trees. Do not kill an animal. You will come across people who have given up the world and are sitting in monasteries. Leave them alone."
Basically, it is permissible to deal with non-Muslims in aspects that help in the progress of humanity, but not in those that involve transgression and injustice. The Prophet (PBUH) was keen on joining alliances that support what is good, and fight what is unjust. He (PBUH) said: "I witnessed an alliance in Jaahiliyyah (pre-Islam) in Dar (house) Ibn Jodaan and have I been invited today, I would have accepted." [Akhbaar Makkah.] For Al- Bayhaqi.
Accordingly, it is permissible for a Muslim to work with organizations, whose vision is in harmony with the principles of Sharia, under the umbrella of all that is good and useful to mankind. And Allah Knows Best.