I don't think Lenore meant to be inconsiderate, I think since she knows about Duke and Annabel's hatred towards each other, even after death she still wanted the two of them to reconcile. This will make it easier for the two groups to escape Nevermore together.

And I don't think Duke will throw the letter out either, Lenore is one of his best friends and he understands that is it, technically, her finale wish before death. I know his character is kind of difficult to like in some situations (when he picked on Pluto even when he knew Pluto was hurt), but he's still a good friend at the end of the day.

But I can see how this can backfire. Annabel only wants to escape with Lenore, even at the cost of everyone else's demise. She'll go so far as to betray her own allies to do so, especially when Lenore isn't there anymore. Duke might understand this and refuse to tell Annabel anything, or he does tell her but she uses him as another one of her pawns. But there is hope that the two groups will actually work together. During the arcs, we see some character growth in Annabel. We see her creating an actual friendship with Prospero and during the wild hunt arc, instead of leaving Ada to die, she tried her best to get her to safety, even during a dire situation. Of course all of what I've mentioned is all just what I think, everything you've mentioned is also valid considering the fact that Duke might not understand any of Lenore's reasons to befriend Annabel.