I have an NPC like this in my 3.5 campaign, an illithid that has rejected his people's traditional disdain of non-illithids. He thinks that learning from the lesser races is more worthy than treating them as food, and because of this has shifted to LN rather than LE.
He is still lawful, however, and so he eats criminal brains. He justifies this as being a service to the community he is hiding among, which keeps him from being a parasite, and more of an ally. Combined with a class like Inquisitor or Investigator, your mind flayer could have a similar POV. As long as the PC's and their allies aren't criminals and dangerous to the larger society, they would be relatively safe.
Also, remember that intelligent non-humanoids are likely to be nourishing as well. Dragon brain is likely a delicacy...