Just wondering if I use the above build would Krassis be able to reroll a die on his first attack, hit, attack again, reroll, miss anyway, then activate gunner for a primary weapon attack?

Yes.

Be aware that if the first Cluster Missiles attack did NOT hit (even with Krassis' reroll), Gunner would kick in, and you lose the second attack from the Cluster Missiles, but get a new primary weapon attack from Gunner.