I have thought out the scenarios for the show for awhile
they don't always pan out, but the writers do a pretty credible job, keeping it real
Gus (Chicken guy) is a ruthless business man, with pretty flawless execution
Gus prefers to deal with people like the cartel boys, they would cut off their own leg before they would give anybody up and risk their families.
Jessie is a 20,21? year old at most, immature, drug user. Gus can't risk leaving him out there, especilly after Jessie has seen him and knows who he is. Jessie has no controls,
Walt has been fairly reliable for Gus, he is 'pragmatic' he throws that word at Gus, too. He has a wife and two children, these are controls for Gus to use.
However, lately with Walt's emotional involvement with Jessie, he has acted less than 'pragmatic or rational' for that reason Gus may even find Walt a threat. If Walt got caught would he do the 'pragmatic' thing and roll over on Gus, if he thought he could arrange witness protection for his family?
Jessie is the 'fly in the ointment' he is the one putting everyone at risk.
If something happened to him the rest could reach an accommodation.