What do you mean, give them back channel energy?
You mean ignore the fact that you traded that in for another power? No, as a GM I certainly wouldn't allow that.
However, I would allow you to take a level in wizard with the necromancy sub-school and pick it up, which is normally allowed.
Alternatively you may consider training out of the archetype, as it's not very good in the first place. Of course what you lose isn't great either...so it's relatively a wash.
If you found an archetype that gives Channel Energy to replace the Channel Energy class feature that you traded away with your current archetype, would that not be two archetypes altering the same class feature and therefore ineligible as a selection for your character?
see if you can talk your GM into allowing you to VMC, VMC Wizard for the Necromancy power should work, or Cleric for the channels they have
Assuming most of your undead are mindless melee attacking machine the +5 to initiative isn't that big a deal. If they have to move to the enemy they don't get to full attack, whereas if the enemy goes first they get to full attack them first.
And honestly, if you're doing it right none of your minions ever perish because they're all bloody skeletons.
And also, initiative doesn't really control surprise rounds. That's mostly a factor of the enemy being unaware of your existence. Which is actually made quite difficult by a large menagerie of undead with what are likely to be poor stealth checks.
If instead you meant rounds where the enemy is flat-footed...well that's true. But I honestly don't consider that especially valuable unless you get sneak attack.
Also, the Undead Lord archetype would be a much better choice for a necromancer cleric.
Doesn't quite work that way (with regard to the weapons).
It's going to be a move action to manipulate the weapons (including pulling it out of the ground, sorry no free action here). Letting go of a weapon is a free action, but picking an item up is a move action. An item on (in) the ground is an item you need to pick up.
It's exceedingly rare for anyone to actually carry Holy Water. I don't think any enemy description actually has them carrying Holy Water. Not to say it's impossible, but it's unlikely. They would need to knock your undead into the negatives, and mid combat stop and pull out the Holy Water to hit the skeleton. Which means they're wasting an action not attacking you or the rest of your party. Bloody skeletons are a superior choice, without question.
As for Death and Nobility...maybe Nobility is a good choice. But many DMs don't allow you to get leadership.
Also, you shouldn't bother wasting animating skeletons on 1 HD things. Humanoids are the worst choice for animating dead. You don't even get the spell till 5th level, so you should probably find 5HD+ creatures to animate. Not things with class levels.