You have no need to be confused. There is nothing at all wrong with putting 'though' at the end of a sentence. 'Though' is widely used in this way, and the construction is entirely correct. I can't understand why you say that 'some people don't like the usage'. It's fine in any spoken sentence, and also in informal written sentences. The alternative word that can go at the end of the sentence with the same meaning is 'however'. This is possible, but slightly awkward-sounding in speech. 'Though' is much more natural. I would carry on using it, if I were you.

I wouldn't consider putting 'though' at the end as less formal. You could say: "It tastes great, but it smells awful"