As you are mainly writing in English your target audience is probably from English speaking countries without a lot of knowledge about Arabic. It's not a common language to learn when compared to something like French or Spanish as far as I am aware of. As such you should be careful about using a language other than English in your text. I am from Germany for example and have never learned to speak Arabic. I would have absolutely no idea how to pronounce the second version, which is a problem for me when I am reading something because it completely breaks immersion. I would need to think about what the character in my head would say and how it would sound. And that's not possible when I can't read the word.
With the phonetic spelling I have a pretty good idea of how the character would say it. It's probably still quite far off, because I can't understand Arabic and wouldn't know a native Arabic speaker would actually pronounce it, but I would have an idea. And that's what I need to stay immersed in the story.
Especially when you are doing this more than just once or twice I would be careful. The second version is factually more correct than the first one, but for people who can't speak and read Arabic it's impossible to have a feeling for how your character sounds, which many people don't like.
You could also try to get around this whole issue by describing what he really wants to say with an addition that he is saying it in a different language than you are using for the reader's convenience. Something like:
'Relax' Essam said to himself in Arabic, taking a deep breath and tossing the book onto a nearby table.
It's easy to do and won't lead to any kind of confusion. Because the first version you propose could lead to a bit of confusion with people who speak Arabic and might wonder what word you mean exactly with the phonetic spelling as it's written completely different from the "real thing". And your second version will lead to confusion with people who don't speak Arabic, because they won't have a clue about how to pronounce that and whether they got the meaning right from the context.
There is no "correct" way. Only different ways with different levels of clarity for different target audiences. For the general English speaking public you just want to be careful with incorporating different languages into your text.