Regarding the actual judgement and its philosophical background
The constitutional court in fact had three main points in its justification of the judgement:
- Because you can never now if your actions provide the desired outcome, i.e. if the alternative would really have been worse. You produce facts and exclude the possibility of probably better alternatives by this. Do you know that the torture will make him speak? Do you know it does help anything because the victim is not already dead? Do you know that the men and women on this plane will not decide themselves for sacrificing their lives or can overcome the terrorists? No, you do not. You only claim to have this knowledge you cannot possibly have.
=> Kantian point against consequentialistic reasoning, e.g. in his On a supposed right to lie from philanthropy
- Because you would help them show that you are in no sense morally superior, giving up your values you pretend to hold higher than anything else if it fits you. Therefore it would help the cause of the terrorists.
=> I am not aware of any particularly philosophical writing that adresses this argument, but it seems good.
- Legally, there is no alternative! The highest value of German constitution (Grundgesetz) is human dignity (article 1, sentence 1), not human life (article 2, sentence 2). Torture as well as weighing up lives (plane example) does not take human dignity as absolute value for granted, it rejects it. The German constitution (alongside with the Universal Declaration of Human Rights and the Charter of Fundamental Rights of the European Union, btw!) forbids calculus like this.
=> This also corresponds with the strong kantian tradition in Germany, because the human dignity as inviolable, absolute value is a kantian concept first expressed in his Groundwork of the Metaphysics of Morals (1785), Ak. 435. The very first formulation of dignity in this sense is by Samuel von Pufendorf more than 100 years earlier in De iure naturae et gentium libri octo (1672) as a reaction to Hobbes' Leviathan, so that v. Pufendorf can be considered the ancestor of dignity and public international law [Völkerrecht] in the modern sense.
Regarding the ethical principles and consequences
So the philosophical point behind this reasoning (and the three probably most influential formulations of human rights of the last 70 years) is that while other fundamental/human/basic rights (whatever they are called) can be relativised, the one that constitutes humanity as such, human dignity, must not. And this is in the end a thought that emerged in the era of Enlightenment, embodied by kantian moral philosophy.
Yes, there may be consequences that some individuals hold to be unintentional and undiserable. It will have negative consequences for the welfare of individuals that seem injust. But this is the framework of values we have given ourselves and made them constitutional for our society exactly because it is thought (with Kant) to be the best for human society as a whole. In fact, injustice will be done either way, because the causing acts are injust. This is why we need law (this is the standard thought e.g. of Kant, Fichte and Hegel in their philosophy of law).
Books on that topic
Regarding Kant's own reasons for and conceptions of human dignity:
Sensen, Oliver: Kant on Human Dignity
Regarding the kantian understanding of human rights and the relations between these frameworks:
Follesdal, Andreas and Maliks, Reidar (eds.): Kantian Theory and Human Rights
Appendix regarding the German constitution in particular
The only way to change this in Germany is making a new constitution, because article 1 and 20 cannot be changed and are eternal as long as this constitution is in effect (Article 79, sentence 3 Grundgesetz). This includes the human dignity as highest, absolute (i.e. not to be relativised) value (article 1) and the main rules for the government: Federal structure, rule of law, democracy, representative government, sociality and the right to resist against anyone who actively tries to change any of these (article 20). Perhaps you can now conceive how important it was for the men that formulated the Grundgesetz not to open dignity for ethical calculus, especially after the cruelties and terror of WWII that showed how important the absoluteness of dignity is.
If you are interested to learn more about the structure and values of the German Grundgesetz (basically, the first 17 articles represent the valuation of basic rights according to their order), there is an official translation available (also in PDF) here.