Their meanings, though different, aren't exactly opposite. Also, in most cases, you would know which word was being used by understanding the context of the conversation and the syntax of the phrasing.
I don't think these words are often confused in regular use.
You can be discreet when someone doesn't want you to draw attention, and you can be discrete from the party to do so. It's the same with many other words, such as
there,
their, and
they're and a number of other homonyms. They might be confused when we spell them out, but they're not always mixed up in conversation.
If anything, this can be a problem in written communication. Even then, the erroneous sentence might be viewed with criticism and reinterpreted.
List of commonly confused homonyms