although the negative energy burst visual effect is cool, it could lead to OMG EBOL from metajerks. slipping a skeleton to the end of the party list is cool. but i dont know about this current setup.

When an evil-aligned cleric calls upon the power of his patron deity to Rebuke or Command Undead, it is apparent to witnesses that he is doing something fundamentally different from when a good-aligned cleric calls upon the power of his deity to Turn or Destroy Undead. There's no metagaming involved.

Basically -- if you wish to hide your allegience from your companions, don't openly attempt to Rebuke or Command the Undead.