Yes, they are annoying. I am a big fan of the fluff so its always troubling to see a paint scheme totally unsupported by the fluff. Custom Space Marine chapters with accurate fluff support can be very cool and enjoyable to play against as one basically only sees First Founding chapters running around these days.
However, I would think, if you don't like red, then get a new force. I have a Crimson Fists force and part of what makes them so enjoyable to paint, play with, and read about is their paint scheme. It would seem a bit odd to run against a force of Crimson Fists that has purple armour. Not a different chapter, just purple Crimson Fists. Or blue Blood Angels, for example. Why not choose a force with a scheme you like instead of making one that doesn't fit?
For example, what about a force of Khorne Berzerkers that has sworn allegiance to Abaddon and painted themselves in Black Legion colors, with perhaps only one shoulder pad painted red. Such a force is totally sanctioned by the fluff and easily fits in, making a cool back story.
Or perhaps look to the Chaos Renegade warbands. They are numerous and are formed from Traitor Marines all over the galaxy and could literally be any color scheme.
They are your models so you can do whatever you want with them, but that doesn't mean I have to like it.
Of course the worst models are the unpainted ones. So just by painting them, they will be better than most other models out there.