The discussion about Ejector Seats is remarkably like the one that goes on these days with regard to Lifeboats (rather than Liferafts) on ships. The balance is one of weighing the benefits of the rescue system (in the case of Lifeboats they are extremely rarely used in anger these days, even in emergencies) against the cost, effort and real risks (Ejector Seats can kill, and Lifeboats, which have to be tested on a regular basis, can and do kill those testing them).
The basic problem is that no aircraft, even new ones operated and maintained to the highest standards, is immune from the unknown and unpredictable. Stuff happens, even to RAF jets pootling along doing a relatively sedate transit - for a start parts lives are estimates and the odd one will fail earlier than expected. After all, even if you maintain your car to the highest standards and drive it very carefully there is still the risk that the engine will conk out (or it will catch fire) when you least expect it - and when the equivalent happens in a Fast Jet there is no nice safe Hard Shoulder to pull over on to.
The above also ignores the 'other bloke' effect. The car that pulls out from a driveway masked by hedges, straight into the side of the car, the aircraft that removes one of your wings as he comes up from a blind-spot (it happens). Or the bird that decides to fly up in front of your aircraft and take a trip through the engine - it happens, even with lots of effort to avoid the situation. Fly an aircraft long enough, drive a car long enough, dive deep enough often enough, and you WILL have an emergency of some kind. If you have left an item of emergency kit behind (I don't know enough about diving to suggest a representative item) you are, at the very least, going to look a bit embarrassed, you might end up dead - and so might people on the ground if your 'perfect plane' comes down in the wrong place.
And therin lies a point. Fats Jets are not designed to be easy to leave with a dead Ejector Seat, if its possible it takes a long time, time which a pilot can't use to try and ensure his aircraft doesn't come down somewhere bad. Give that pilot an Ejection Seat, especially a modern one, and all of a sudden they have more time before they have to make the fateful decision 'my life or theirs' in which to ensure that the decsion never has to be made. Historically pilots in that situation seem to have opted to save lives on the ground but why rely on uncertain behaviours if you can encourage the right behaviour by providing safety equipment?
Going back to the first paragraph, its a case of balancing risks (and costs). Ejector Seats on Civilian Aircraft haven't killed that many people (none that I'm aware of) and are an item of Safety Equipment that was designed into the aircraft. The balance might change in the future, particularly with the withdrawal of MB support for older seats, but at the moment the suggestion that the seats should be deactivated is akin to saying that self-inflating Lifejackets (automatic or manual) shouldn't be worn because the pressure bulb might injure someone in some way, in certain scenarios they can trap people and they cost time and money to service.
(Yep, long-winded again! - Sorry)
 I'm thinking of a few aircraft fires (not the Nimrod one), each one different, some resulting in fatalities.