The short answer is that there's no good evidence that Luthor was intercepting Keefe's cheques and good evidence that Keefe was returning them himself.
In addition to the fact that Keefe would have been well aware of the Wayne Fund and there's really no good way that Luthor could have kept that information from him or explained why his cheques weren't coming through, most critically Keefe has an anti-shrine to Superman in his basement and regularly boxes off Superman's name in the same blood-red marker that's used to scrawl hate messages onto the cheques that he gets from the Wayne Fund.
That being said, Luthor does refer to ...
"Little red notes, big bang. You let your family die"
... in his conversation with Superman, so it's reasonable to assume that he was responsible for the final note that Batman/Bruce received.
You might also want to note that the final letter is atypical of the others. All of the previous notes were written directly onto cheques. All were written with some variant of Bruce, Wayne or B. at the start of each sentence and the handwriting in the final note is subtly different from the cheques.
BRUCE WAYNE OPEN YOUR EYES, B. WAYNE I AM YOUR GHOST, BRUCE NO TRUCE,
B. WAYNE I HAUNT YOU, BRUCE WAYNE = BLIND
YOU LET YOUR FAMILY DIE.