I disagree. If I go outside now and happen to see an elephant it doesn't mean elephants are common in North America. It just means I happened to see a rare occurrence. So long as the narrative acknowledges it as a rare occurrence that is how it should be treated. A single helpful Illithid found in the Underdark does not mean helpful illithids aren't rare anymore. It just means you witnessed something unusual.
Beyond that if you were going to run into a mind flayer not aligned with the colonies the Underdark is a very loreful place to find him. The Underdark has a fairly massive mind flayer population, and renegade mind flayers are a thing that can and does happen. They also tend to learn arcane magic to help shield their minds from falling under the sway of an Elder Brain again, and this one just so happens to have joined what seems to be an organization of wizards.
There is nothing about Omeluum that is especially lore breaking or entirely unique. Just rare. And the location and conditions we find him in are pretty typical for a mind flayer in his position.
I'd also like to throw out that him helping us doesn't necessarily make him good. We're basically allowing him to run experiments on us, so it isn't like he's doing this purely out of kindness.