The judge ruled there was no violation of their constitutional rights, explicitly because Congress was involved in authorizing military action against the wider threat and specifically in this case Congress was in the approval process for authorizing individual targets.
There was no violation of checks and balances here. That is not to say other uses of the so-called "disposition matrix" might be challenged in the future, but at least in the cases of these individuals, the courts have ruled that no rights were violated.
Ha! So far it's had a pretty good history, and 4 American citizens have been killed from it.
- Anwar al-Awlaki - Abdulrahman al-Awlaki - Samir Khan - Jude Kenan Mohammad
Their due process, as enumerated in the constitution was conclusively violated; and only one (Anwar) was targeted due to involvement in Al-Qaeda.