Some atheist groups are unhappy that they are being met separately (though they would prefer that religious organisations would be treated like NGOs), especially with the Freemasons, who they've ridiculed for their rituals and dispute their secular nature. Personally I find the whole thing a bit irrelevant. I don't mind these organisations being met together; it's a bit silly to see the Catholic Church worried about a "heirarchy of religions" - monotheistic ones are ok, but it's dangerous and overly "religiously correct" to include Hinduism, etc.
Ultimately, I think that there should be some consultation with religious organisations because they are a part of our society and culture. However, I'd object to the requirement for their consultation to be interpreted any more widely than a yearly summit or a few meetings on matters of interest:
"Beyond the annual summit, religious leaders interpret Article 17, which commits the EU to holding "an open, transparent and regular dialogue with… churches and non-confessional and philosophical organisations", as meaning regular meetings with senior civil servants, not just on grand themes such as Monday's topic of the battle against poverty, but on more concrete legislative measures dealing with climate change, education, immigration, social services and labour laws."
Going this far would be giving them too much access (though it's hard to say if influence would necessarily follow). Occasional consultation on matters that might directly impact on religious groups or practice is a good thing, but the separation of church and state needs to be maintained.
I just feel sorry for all those conspiracy theorists who might have injured themselves with excitement at the news of Freemasons and European summits...