Don't know that he had kill orders as if you recall Gambit went back in time and visited Sinister and Sinister realized Gambit knew him. So Sinister likely knew that Gambit had not gone back in time yet during the MM so couldn't kill him as if he had then Sinister would never have acquired his shape shifting powers from Courier. Unless of cause Sinister presumes that in a multiverse you can't have a grandfather paradox.
Of course this is all a retcon but it seems Sinister sought out Gambit most likely because of the fact he visited him in the past.