well, good if you only have a few who have problems with it. the only real way to get a different meaning through text(messages), is marking the text in any special way. most likely smileys, in excess.
i am asperger, but a good amount of my friend are very nt and they have problems with this aswell(mostly when the mssage lacks smileys but sometimes even with them).
you can try to teach them the way smileys interact with typical messages, but beyond that i dont think there is much you can do.
hopefully it helps