Smokie killed the pilot because Seth was of no use to MIB.
This conclusion is based upon examination of the two characters and their relationships.
Smokie. Who did he kill and why? In retrospect, he didn’t seem to kill out of rage – he seemed quite methodical and quite calm when he apologized that Ben had to see him like that.
Those killed seem to be grouped into two major groups: those that attacked him; those that couldn’t be used by him (e.g. the temple) – kind of a ‘if you’re not part of the solution, you’re part of the problem’. [I believe all of the people killed could fall into these groups except Mother – who was directly preventing MIB from leaving.
Seth. Not a candidate, never was. He was a ‘good guy’ (long time married, and I think Lapedeus said something like that). MIB likely scanned him and decided he wasn’t ‘controllable’ – he ‘wouldn’t go along’ (If this is why Eco was killed, MIB’s scanning wasn’t to judge good/bad but judge their character and malleability … and usefulness in the one thing MIB wants … to get off the island and ‘go home’.) Indeed, some of the information about how they got ‘Lost’ (or perhaps help them get found w/o MIB) just might have messed up his loophole.
Though Seth was a pilot, the plane itself wasn’t pilotable. Not useful.
Good guys can’t/won’t kill candidates. Not useful.
It was either that … or his breath.