Does it? If I see a character coloured with blue hair on the chapter-cover art - which is reasonably the first piece of art I see when I start reading a chapter - I am going to go into the chapter with that piece of information already slotted into my head. The immersion won't be broken. And if she shows up partway through a chapter, and is only appearing coloured on the cover of the next chapter, I will just re-adjust my perception of the character and move on; I'm going to go out on a limb and say that most of your readers will do the same.
Also, no matter what you do, you won't ever be able to fully control the readers' expectations and reactions. Even choosing colour won't fully fix this. Like it or not, creating the story is really only half the work; your audience does the rest. You can do your best to present the story in such a way that they will most likely react in a certain way - but storytelling has always been at least partly a participatory medium. You can't fully control what happens inside the heads of your readers - nor, do I think, should you want to - because a lot of why people enjoy stories are because of what they read between the lines. And what they read between the lines depends as much on them and their personal experiences as it does on you as creators.
Yes, colour is a powerful tool - but so is black and white. It depends on how you work with it. And if you really hate painting, then you shouldn't be forced to paint. You can be just as expressive in black and white as you can be in colour, just in a different way.
As for @Terraset's point 1.) - I'm doing a long series. Grassblades will hopefully clock in at under 1000 pages. And I'm doing it in full colour. Most of the longer-format webcomics I read are in colour - Blindsprings, Evan Dahm's Vattu, , Zack Morrison's ParaNatural, Wilde Life, Monsterkind, No Need for Bushido, Cucumber Quest etc., etc. Doing a comic in full colour will not make you stand out any more, or any less, than lots of other comics.
And yes, full colour is a lot more work. If your artist feels uncomfortable working in colour, it's even more hard work than it is for someone who is comfortable - and the project you're talking about supposedly runs to about 500 pages. We're talking years of time to complete that - do you really want to put your artist through doing something they claim to hate for that long?
If you absolutely, seriously have to have colour, I suggest finding a second artist to colour your comics - this will lighten the workload on @spudfuzz, and will likely result in the comic being produced faster, without anyone having to do something they despise doing.