Why were the samurai ordered to commit suicide?

They were on the wrong side of a clan dispute. Once resolved, they were probably considered to be untrustworthy because of their prior allegiances, so suicide (Sepuku) was ordered for them.

I guess it's the honourable thing to do, plus you don't want a possible rebellion splitting the clan in half, with your own highly skilled fighters going against you at a later date. This way you guarantee discipline as well as finding out their intentions even if it means self sacrifice.