You're referring to a court ruling, not a political decision. A court does not decide on policy, it must apply the existing law.
The applicable law is the EU VAT Directive (Directive 2006/112). As originally written in 2006, clause III.6 stated that states may apply a reduced VAT rate to
(6) supply, including on loan by libraries, of books (including brochures, leaflets and similar printed matter, children's picture, drawing or colouring books, music printed or in manuscript form, maps and hydrographic or similar charts), newspapers and periodicals, other than material wholly or predominantly devoted to advertising;
In 2009, the wording was amended by Directive 2009/47 to
supply, including on loan by libraries, of books on all physical means of support (including brochures, leaflets and similar printed matter, children’s picture, drawing or colouring books, music printed or in manuscript form, maps and hydrographic or similar charts), newspapers and periodicals, other than material wholly or predominantly devoted to advertising
The court's 2015 ruling explains (in more detail than the press release) that since the law explicitly limits the clause to books delivered on physical means of support, and another clause explicitly states that the sale of electronic services is subject to the ordinary VAT rate, the law cannot be applied to the sale of e-books. A similar 2017 ruling upholds this interpretation.
The rationale given for the 2009 change in wording is that
Category 6 (books, etc.): The current wording covers only books on paper support. For reason of neutrality, an extension is necessary in order to also cover books that are on CD, CD-ROMs or any similar physical medium that predominantly reproduce the same information content as printed books. Thus, only recordings that fundamentally reproduce the written text in a book are covered. A recording that includes supplementary material such as games, search functions, links to other material and similar, apart from the text read aloud, continues to be subject to the normal VAT rate.
It is strange that a change of wording on the rationale that what counts is the information content and not the delivery medium explicitly limited the clause to delivery on physical medium. I can't find any discussion of this matter (but I did not search through any parliament or commission transcripts to see if there ever was a debate on this topic).
Several EU countries (including France which now argues for lower VAT on ebooks) have a public policy of favoring dedicated bookstores with competent vendors over remote sales and bestseller sales at magazine stands. It's possible that restricting the lower VAT to physical books only was done as part of this policy (since ebook sales would never benefit bookstores), but this is pure speculation on my part. It's also possible that nobody was thinking of ebooks when writing this directive: in 2009, they were still a pretty niche market (I don't have figures for the EU, this site states that only 2% of the US reading population had an e-book reader in 2009). It was also uncommon in 2009 to consider environmental benefits outside energy consumption and direct pollution, and it is still far from systematic even in the EU to take environmental impact into account when economic matters are at stake, so your ecological arguments would not have been prominent in any political discussion about e-books vs paper books. (Plus electronic devices and their energy consumption aren't green either.)
According to VATlive, there now seems to be a consensus to amend the directive to include e-books in the lower VAT rate. A proposal was made in 2016, and has been blocked so far only because it was tied to other changes that were not consensual.