Their reaction to an Andalite landing in front of them kind of proved they weren't Controllers, but also the fact that he saw 5 lines join his brother's when the Ellimist moved him through time/space. Obviously these 5 humans were those lines, so he knew he could trust them.
Besides that, it was simply a calculated risk. If he did nothing, Earth would've been screwed, so what did he have to lose by giving them the morphing technology?