And I believe Khan didn't know the torpedoes were the ones containing his crew until Kirk told him how many he had (or some such). So not part of Khan's plan (he thought his crew were already dead anyway didn't he, hence his bad mood?) and it didn't seem to make sense from Marcus' POV either.
Of course Khan wasn't certain what Marcus had given Kirk. Khan wasn't there when the Enterprise
All Khan could do was light the fuse and hope that Marcus would unwittingly play along as Khan hoped. But when Khan heard how many torpedoes Kirk had, he knew what he hoped would happen had in fact occurred: he had managed to get his people smuggled out of Section 31.