Dead people are dead Shaker
I know.
how can any decision taken after their death have any effect on them?
On them directly, as a person? It can't. They're dead. You can stain somebody's memory, however, by giving them a funeral that makes a mockery of their professed beliefs in their lifetime. If somebody is a known atheist, what does it say to the mourners at the funeral and what does it say for the relatives if they arrange a religious funeral? That same point works equally well in reverse, incidentally. At the risk of invoking some sort of internet law, the Jimmy Savile affair demonstrates what can be done to a person's memory and reputation after their death.
Non-religious funerals are rising as it is; there's a case to be made that the visibility of non-religious funerals of several high-profile people in relatively recent years (Ronnie Barker; Bob Monkhouse; Linda Smith; Dave Allen) has helped this process by making people aware that such an option is available. When somebody dies many if not most people are too busy with their grief to want to get stuck into the niceties of funeral planning, which is why there are still so many people content to sit back and let the local vicar step in and take the wheel even though the dear departed never darkened a church's door. Reading around non-religious funerals, one of the most common things said by those left behind is: "I didn't know we could." If there is such a thing as society, no decision no matter how seemingly personal is made in a total vacuum. You can't do anything for the dead aside from put a full stop to their life by giving them a send-off in keeping with it, otherwise you're pissing all over their integrity to give yourself a warm little glow.
Of your scenario happens, the only people to be annoyed/upset or angry would be still living atheists who can't quite accept the truth that dead people are dead or who would regard the trappings of a religious funeral as a waste of money.
I think a great many of the trappings of most funerals religious or not are a waste of money. Like the veterinary profession, it's a money-making racket. Still, there are certain legal and practical niceties to be observed.