I think that one of Mishima's primary motivation, what he is trying to say and what he is trying to get at in this story, is the praising of following duty to its natural consequence.  The protagonist, Takeyama, is in an impossible situation in that he is poised between his unit and his loyalty to the government.  In this, Mishima suggests that suicide becomes a way out for him, a way to maintain his honor as opposed to having it become negotiated and sacrificed, to an extent, in the real world.  Reiko is placed in the same predicament, having made an oath to follow her husband in death.  Mishima withholds judgment on what both should do, except in describing their procedures towards suicide and the actual act itself in glowing terms.  The "peace" within both as they both accept what has to be done is Mishima's primary motivation in praising such an action as an honorable one, a condition where purity is still intact.  For Mishima, the world he creates inPatriotismis one in which impurity is evident.  The soldiers who break ranks and mutiny against the government have dishonored their code of loyalty.  Yet, at the same time, to side with the government against that of one's soldiers and fellow men in battle is equally disloyal.  It is for this reason that Mishima constructs Takeyama's situation in terms that isolate him from both notions of solidarity:

I shall be in command of a unit with orders to attack them. . . . I can’t do it. It's impossible to do a thing like that.

For Takeyama, the only unity present in such a divided consciousness is through suicide and the glory of approaching it with the mentality that it takes internal strength to seek such transcendent unity.  For Mishima, this exaltation becomes the primary concern, one that does not consider "finding" a solution but reveling in an Ancient code of conduct that transcends the current contingency of mutability and pragmatism.