For all his faults Jimmy was a good earner.
Lufthansa is case in point. I expect Jimmy kicked up quite a bit of money to Paulie.

Tommy's fate should have served as a WARNING to Jimmy (and Henry for that matter) that if a Sicilian was dispensable then no one would hesitate about knocking off a couple of Irish guys.

Better to dispose of 1 guy and use it as a warning then dispose of more good earners than you need to. It should have been enough to bring Jimmy into line, Paulie didn't yet know that Jimmy had helped Henry with the drug deals.

Also remember that Jimmy and Henry could never be made - so would never have become decisionmakers.
Tommy could have been promoted, but was less dangerous dead.