I have a completely different read on the situation. At first, I don't think 50 particularly cared about Ja at all. If you listen to the OG version of
Your Lifes On the Line, which officially sparked the beef, 50 dissed Mr.Cheeks, Onyx, and Ja. When you take that into consideration, the song plays more as a continuation of 50's naming-names gimmick which he popularized with How To Rob than a singled-out attack on Ja. Thus, it makes more sense to deduce that the song was meant as a spiritual successor to How To Rob but theme'd around known rappers from 50's hood which just so happens to include Ja.
There is also more evidence that bolsters this conclusion too. For one, when Ja asked 50 in ATL why he dissed him, according to Ja, (paraphrasing here) 50 claimed it wasn't personal, the record was just a tool to get his name out there and there is nothing he can do to take it back once it went out. Also, in
Be A Gentleman which acts as part 3 in 50's naming-names series in which he focus on Jay-z, he states this -
"
No more freestyles and verses killing Sticky and Ja
I'm moving on now, I got bigger fish to fry
Since How to Rob, a lot of nikkas been naming names
Monkey see monkey do, I done changed the game"
Again, I think these bars make it clear that Ja was just a tool 50 could utilize for his own self-interest. I don't think 50 had any personal ill-will or anything against Ja the person, he was just determined to do anything he could possibly do to build a buzz, and at this point in his career, How To Rob was the biggest record he produced so he was focused on recreating that record over and over to sustain that buzz for his LP.
And the only reason why Ja became 50's prime focus later on out of all the dudes he dissed prior was because Ja physical checked him on more than one occasion for his disrespect, and beefing with Ja resulted him being blacked-balled to a degree, stabbed, shot, and chased out of NYC. The hatred stemmed from 50 having to face the consequence of his own actions, unfortunately he ratted as way to escape the beef.