Even if he is stronger than Piccolo, I doubt Kaioshin's strong enough to do any kind of damage to this incarnation of Trunks. I'd say the power gap is big enough that even with his decreased speed, Trunks would still end up faster than Kaioshin.
Regardless of their direct speed abilities, Kaioshin does have a superior version of the Instantaneous Movement, so I give him a speed advantage when it comes down to the nitty gritty.