If Jack had helped young Ben, he wouldn't have gone to the Others to become who he is today.
Not necessarily. If Jack had agreed to helped with Ben then the timeline would have self-corrected and events would have still played out more or less the same.
Example: Jack agrees to help, but on the way to the infirmary he trips on a rock, smacks his head on (insert random object) and is knocked unconscious for a long period of time. Events play out the same as if he had not agreed to help.
Not the best example, but you get the point. Jack is not to blame. Sayid is not to blame. Whatever happened, happened.
So why doesn't Desmond remember Fairaday?
Because the writers didn't know that they were going to meet up back in time when they first wrote scenes with those characters. Just like they didn't know when Sayid & Ben first met that they would eventually have Sayid shoot Young Ben. That is why we are getting all of this forced explanations that "Desmond thought it was a dream" and "The process to save Young Ben will make him forget being shot", yadayadayada.
Since these specifics wern't worked out exactly 2+ years ago, and since their style of time travel is "you can't change anything" then we will keep getting situations where they will make/force people not to remember events that they should remember. It's just the nature of writing a long running seriaized tv series.
I mean, maybe
they knew back in season two & three that in season 5 some of the main characters would be back in time in the 1970's dealing with Dharma. And maybe
(and this is a big maybe) they even had the idea tat someone would shoot Young Ben... but for all we know it was going to be Mr. Eko or Ana-Lucia that they had planed to pull the trigger and then when those actors had to suddenly be written off of the show they had to change their plans. Now Sayid is the shooter and since they wern't planning on that, that's why they have to make sure that it Ben doesn't remember who shot him by having the "process" erase his memory. It's the only way to tie up those loose ends.
But I still doubt they had this fully planned out back then. They probably had a general idea of what was going to happen, but no specifics since at that time they didn't even know how long the series was going to go on for (7 seasons with 24 eps. each? 8 seasons?) they didn't know. They also didn't know which actors would still be around by the time they got to telling this part of the story.