That's a lovely story, but we're not talking about one hours worth of pay here.
It'd be interesting to know what sort of fees the BRK pilots are being forced to pay for this setup and how the management of their money actually works.
Being a contractor is actually very simple, just set up a ltd co. (just a few quid) register for tax, N.I and VAT (if applicable) and get an accountant to sort everything out. A good accountant shouldn't cost you any more than £80 a month.
Other fees are then your public liability, employers liability etc, but that shouldn't be more than £400 a year even for someone who works airside. (Obviously!)
If you haven't got control over who your accountants are, then I can't really see how you are a seperate ltd co. Don't forget that as a contractor, you are both the director and employee and so how you can be forced into this sort of thing baffles the mind.
It doesn't make sense for BRK/RYR either unless they are using it to make money or exert control. Using contractors is usually done as it's the simplist way to get decent staff at short notice. It's usually a bit more expensive long term than having employed staff, but contractors give you much more flexibility and control over your costs. This is not normally to the employees benefit obviously!