It's not that bad
The council is bureaucracy overruling the Parliament, thus invalidating the very principle of democracy. We have seen this in action with the new EU Patents law: the Parliament had passed several amendments to the original proposal, yet the Council ended up ignoring those democraticly voted amendments and passing an even worse legislation than the original draft. This is clearly different than what happens between a higher and lower chambers each examining new legislations before it is ratified.
Martin-Eric, it's nothing that bad. The council of ministers did indeed vote differently, but that happens routinely between a higher and a lower chamber. I remember having seen a reaction from Bart Staes, Belgian MEP for the Greens, but can't find it anymore; he explained, though, that the law will now have to go back to the parliament again, and that it won't pass unless both the council and the parliament agree.
Sounds very much like a lower and higher chamber to me.