His only alternative would have been to have gone renegade, moving the whole familly beyond the reach of the Imperium.
Leto suspects a trap, yes, but he doesn't know or suspect its true magnitude. House Harkonnen, an enemy of House Atreides, is expected to have left booby-traps, and to attempt to infiltrate the house-guard and generally mess with spice production operations, but he thinks that he can turn the situation around to the advantage of house Atreides.
The agreement between the Landsraad and the Imperium prohibited the emperor acting against any individual house openly, and Leto trusted that no Emperor would be so bold as to risk censure by the other great houses by acting this way.
Leto only discovers the true monstrousness of the conspiracy between the Emperor and the Baron when the House-shield has already been taken down and it's observed that some of the attacking troops, men in Harkonnen livery - were imperial Sardaukar in disguise.
That's also an explanation for why the Emperor's troops were disguised, so as to attempt to hide the Emperor's hand in the matter, and why Paul proposed to bring a "Bill of Particulars" before the Laandsrad High council, to show the Emperor's hidden guilt.