The government would never have access to a phone with a compromised version of an OS that they could use to repeat this trick. Rather, the government would have to obtain court orders and have forensics done under supervision.
This isn't a backdoor and doesn't affect consumers, and sets a really high bar to trying to scale this for the government because it requires Apple as the gatekeeper every time to agree to do the one-off hack.
The cynic in me thinks that this letter is more about brand image. Apple wants to claim they can't hack their own phones, even if the government asks, but clearly in the case of the iPhone 5C it IS possible for them to do it, and this creates a contradiction with their public marketing and privacy position. If they didn't release this open letter, then simply complying with the judges order would make them look bad.