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Most specifically in terms of colour schemes... are there differences? Can fluff nazis accept GKs that deviate from the main colour scheme?

The only difference I can think of is the purifiers having white helmets, but they're a pretty specialist brotherhood really :/

I'm a bit of a fluff nazi, a fluff fascist if you will (all nazis are fascists, not all fascists are nazis ). But I don't believe there are supposed to be any difference in the colour schemes of the different Brotherhoods, with the exception of the Purifiers all having white helmets.

I am willing to accept a player that has their Grey Knights painted in different colours. Is it the way I'm painting my Grey Knights, no, but if you pick a good colour scheme and do a good job of painting it, I won't say anything against it. It's just not what I would do.

I see no major issue with differently colored Grey Knights. Technically, I'm not sure its ever actually stated whether all brotherhoods are similar color schemes or not. I've seen some pretty good jobs that are actually grey. I myself did one in red and gold as a test. All the rest of my Knights have white shoulderpads, because I hate just having them look like I dipped them in boltgun and then washed them and called it a day.

Purifiers have white helmets, but I think that's the only distinction.

There. The Third Brotherhood's regimental dress.

There was a short period (in an Index Astartes, some time after Inquisitor came out and before Codexemon Hunters did) where Grey knights, like Deathwatch, were primarily black, with only the psychic hoods and the engravings in silver.