Well, Gabriel's the one that gets to decide, but personally I'd see it a bit hard for your character to be able to do that.
There should be a reason behind why evil clerics can rebuke/command undead as opposed to good clerics turning/destroying them. It has to do with what energies keep the undead alive and which ones resonate with the cleric at hand. Undead are supposed to be born of negative energies that go against all life, which is why they are abominations to the living. If your character has enough of this energy type that he can control them, it means that your character is a being filled with negative energies.
While you could theoretically use negative energies for good use, it's a bit of an oxymoron. It's kind of like using the feeling of racism in a 'good way', which technically is kind of a contradiction in that, sure, you could be racist towards a particular ethnic group that is killing your people and use it to fuel your fights against them to defend your people and thus use it in a constructive way, but the thought of racism itself is bigotry regardless, and is not the proper way to think about it (considering that, if there were attackers that were from a favored ethnic group such as those of your people, they should still merit your rage).
It's kind of hard to explain, but pure irrational hatred, regardless towards who it is, is still a negative energy regardless of however it's used. The same way jealousy is a negative feeling, as are greed, and other such things. It's not so much about the way you use them as it is the intent behind them, which is what really 'defines evil', I'd say.
So if you use negative energies for good purposes, they stop being 'negative energies' because they fail to have the negative intent, which is what fuels them.
So again, unless you somehow manage to have a neutral character that can alternate between having evil intents and good intents enough to balance it perfectly, I'd see it very unlikely to have a cleric which is capable of doing that.
There's a difference between clerics and sorcerers/wizards. Clerics use divine energy. Wizards and sorcerers use arcane magic. Arcane necromancy can well be used from the hands of a good wizard, because arcane energies do not rely so much on the soul of a person, more or less, but on arcane energies that are completely neutral to everything. Divine necromancy, however, relies almost solely on the soul of a person, and thus pretty much requires the malign intent behind it's use.
Perhaps you're better off cross-classing a necromancer wizard/sorcerer with a good cleric? Just suggesting.