I would have thought that telling you exactly how it is is rather good leadership? Would you have preferred it if he had lied and told you that the CAS would cry himself to sleep at night if you left?
The RAF as an organisation doesn't really give a **** about you as an individual, if it did it would probably pay better, not be fiddling with pensions and have a 'career management' organisation that actually had the capacity to career manage individuals rather than simply match names to posts. But I doubt BA or Easyjet really give that much of a sh!t about you individually either, they are just in a position to generate profit and pay their staff sufficiently such that an exodus of pilots doesn't effect their ability to make ££s.
Ultimately an organisation cares about its masters; for a company, that is the board and shareholders, for the military it is the politicians. Yes, we could solve pilot retention overnight by paying us all £150k a year, but the politicians don't want the press generated by pilots in air conditioned cockpits (or non-air conditioned 50 degC cockpits for SH guys) getting paid 5 times some soldier that spends his days dodging bullets and IEDs, so they don't do it.
Personally, I have a very good chain of command that I believe would show genuine remorse if I PVRed tomorrow, even if the RAF doesn't collectively weep for me. I enjoy my job, the lifestyle that goes with it, the people I work with (or most of them at least) and happen to think I get paid pretty well for a non-grad who hasn't had to pay a penny for flying training, work clothes, gyms, doctors, dentists, travel etc for 15 odd years. Oh, and I can get a pension next year. Granted, it isn't what it used to be but who the hell else gets a pension at 38 that is well over half the UK average annual salary?!
I think pilot retention is reaching the point that the politicians will start to care, so I think we will see some changes before too long. But if you don't enjoy your job and think you can get paid more in civvy street then leave; the RAF probably doesn't give a sh*t about you, just don't expect your next employers to care that much either!