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An Ork definitely could work with an Inquisitor. They are rational beings with a developed sense of self interest after all, not unthinking monsters.

An example from the lore would be the Massacre at Big Toof River, where Blood Axe Scouts were hired to support Imperial operations.

Two things too consider;
Orks only respect strength, and too a degree, wealth.
Orks have a 'pack-like' mentality, becoming much braver and more aggressive in larger numbers.

So if you were to justify a freeboota working with your inquisitor I would go with something along the following lines;
The Inquisitor pulled the half dead Ork out of a floating space wreck to serve as a more robust sparring partner for him and his acolytes. After weeks of brutal matches the Inquistor realised that, with suitable motivation, the Orks skills could be put to work serving humanity. Although, he is careful to keep it locked safely away when operating near Ork controlled space.