Arrghh - me & dh are 'anal' about nappies and changing.
We are even very particular about where we will change a nappy. We do not think its acceptable to change on a table or bench where food is prepared or eaten, but know so many people ( including family) who do this.
I can even remember being annoyed about a friend leaving her kids pee`d nappy dirty and open on my couch while she went off and did something else for ages - we would never leave a dirty nappy just lying around

I used to take friends nappies and put them in the bin that I was happy for them to go in and unless it was little bubs poo, I think my friends always flushed it down the loo or took it home.
I`m not sure what to suggest cause it does feel like a hard thing to say - yet it is your house and the way you do things should be respected. I know they wont be intentionally offending, but thats what makes it harder to say I guess? ...and in the kitchen bin - urrg.
Perhaps you just need to come out and say something like, " do you mind emptying that in the loo first?". They may be a little surprised, but I`m sure if they will get over it.

I personally have a hard time asking people to take their shoes off when they come in my house... Ive even told someone it was 'fine' that they had their feet in shoes on the arm of my sofa too ?!!