"[...] If there is a blocking minority against the proposal the rules of procedure give enough ways to express it [...]"
I think that is right insofar as the final and formal voting on the Draft Directive might be postponed indefinitely if so desired by a sufficient number of votes. However, this would ultimatively mean that the entire Directive effectively fails. It would, however, not mean to revive any political option to re-open the "B"-item political debate again. Article 3 of the Rules of Procedure reads:
"[...] 6. The provisional agenda shall be divided into Part A and Part B. Items for which approval by the Council is possible without discussion shall be included in Part A, but this does not exclude the possibility of any member of the Council or of the Commission expressing an opinion at the time of the approval of these items and having statements included in the minutes.
[...]
8. However, an “A” item shall be withdrawn from the agenda, unless the Council decides otherwise, if a position on an “A” item might lead to further discussion thereof or if a member of the Council or the Commission so requests. [...]"
Again it should be mentioned that the custom not to re-open the debate on any "A" item seems not to be codified in the Rules. It is a political usage consolidated by long practice. It would, however, surely cause a major political crisis within the EU if any EU country would challenge this practice.
Nevertheless, I would not be overly depressed if the entire Directive fails. The present state of the affairs without any Directive is surely much better than anything else which comes close to the Parliament's version or, beware, even to the radical political goals of the anti-patent campaigners.