I guess they did, given that even the Defence Secretary was "publicly" questioning the decision (via a leaked memo...) and fighting in the Nimrods corner!
So those with the purse strings in 10 and 11 Downing St clearly took the expert advice, and went against it, knowing full well that in the public eye Nimrod = XV230 accident and subsequent fall-out, and nobody (press or public) will question the fact that £3.5Bn isn't actually being saved by scrapping it, cos its already been spent, and we're actually just throwing this money away!