I personally wouldn't go near it without the opinion of a vet and a farrier, pigeon toes mean extra pressure on ligaments and if a horse is worked hard it might not take it.
It can cause ligament strain but you need to get a good farrier to have a look and tell you truthfully whether they are capable of correcting the foot shape to eleviate the problem! I had a fantastic dressage horse whom was seriously pigeoned toed which I bought rather cheaply because of this. After 18 months of remedial farriery there was a dramatic difference to the horse's foot appearance and its movement and never did the horse go lame because of it.