The Player's Handbook says, "Even if a cleric is neutral, channeling positive energy is a good act and channeling negative energy is evil" (160).
The Divine Metamagic feat, in part, says, "As a free action, you can take the energy from turning or rebuking undead and use it to apply a metamagic feat to divine spells that you know" (Complete Divine 80). The phrase take the energy sounds, to this reader, like shorthand for take the positive or negative energy, that, in turn, sounds suspiciously close to normal channeling of negative or positive energy—making the act of taking the energy—possibly—evil or good, depending on the flavor of energy. However, a DM can totally rule otherwise, and another reader may read this in a wholly different way.
Note that documented, actually-called-out-as-evil evil acts are incredibly rare in the core rules—so far as I'm aware it's just this evil act and "trying to dupe someone into buying a cursed item" (Dungeons Master's Guide 277). Further, given the seemingly capricious way in which spells seem to have been given the descriptor evil—the inoffensive 1st-level Clr spell deathwatch [necro] (PH 217) possesses the descriptor evil, for instance—in some campaigns not even casting a spell that possesses the descriptor evil will be an evil act.
In other words, while the rules say that channeling negative energy is an evil act and, therefore,—maybe, by extension—taking the energy from rebuke attempts to power divine feats is also an evil act, expect table variation, especially if—like in many campaigns—the role of alignment is vastly reduced or even eliminated completely.