"I didn't think anyone would be able to do what he's done for years," Miller told Forbes.
It's not the first time Apple has hired a jailbreaker as an intern. Earlier this year MacRumors reported that Apple gave a summer intern slot to Peter Hajas, who developed a popular jailbreak-notification app called MobileNotifier.
The only reason Allegra gave for going to work for the empire whose restrictions he'd been working to undermine for so long was that working on JailbreakMe had been "really, really fun, but it's also been a while and I've been getting bored."
Apple isn't the only company getting rid of the chief source of security headaches by hiring them.
Last week Samsung hired Steve Kondik, whose CyanogenMod software, which cracks and modifies Android smartphones, and is the most popular of a growing category Google wishes would just disappear.
Samsung didn't say what Kondik would be doing; Kondik only tweeted that he would be working to make Android "more awesome"
If it's smart, Apple will have Comex working to make iOS "more un-jailbreakable."
Whether it's willing to take the gamble that teaching Comex more about iOS security would encourage him to leave Apple and continue making jailbreaking products, is a question only Tim Cook can answer – or could, if he weren't tied up on a phone call with Steve every minute of every day.
At Apple, "freedom" is a relative term.
Read more of Kevin Fogarty's CoreIT blog and follow the latest IT news at ITworld. Follow Kevin on Twitter at @KevinFogarty. For the latest IT news, analysis and how-tos, follow ITworld on Twitter and Facebook.