Recently in a game I'm DMing, the alchemist player used the aforementioned ability to shift a high-ranking thieves guild member to good, got all the information they needed to take down the rest of the guild, and convinced him to surrender to the law to atone for his crimes. He will likely face life imprisonment or death.
The problem comes in when a couple of other party members think that what he did constitutes mind control, and thus an alignment shift on the alchemist's part. I'm a bit iffy on the subject, but I love the moral conundrum the alchemist is in with the party, who are wary of his new(to them at least) ability. I've come to the boards to ask you, my fellow players, your opinion on the subject.
Well, first and foremost, one act, no matter how extreme, doesn't cause an alignment shift. Shifts occur after a significant length of time with consistent behavior appropriate to that alignment.
Secondly, if his alignment shifts ... so what? It's not a big deal; he's not one of those classes that loses or changes abilities if his alignment moves around.
Thirdly, enchantment/mind control effects are not 'inherently aligned'; they have no alignment descriptors. Their use is not an innately good/evil/lawful/chaotic act.
Ultimately, outside of the actual RP between the player characters, this is one gigantic non-issue.