I do not understand why Lama Zopa Rinpoche chose to think that those who practise Dorje Shugden is against the Dalai Lama and at the same time, Rinpoche also negate the holy practice and lineage from his Guru, Lama Yeshe.
Rinpoche is not only advising people to not practise, but went to the extent of firstly, explicitly stating that potential students should check whether their teacher is against the Dalai Lama in terms of practising Dorje Shugden, and secondly, implemented the policy of not inviting any teachers who practice Dorje Shugden (Sorry, but Lama Yeshe practices Dorje Shugden, so does it mean he (and incarnation) is NOT welcomed at FPMT centers?).
I'd like to quote a teaching of Lama Zopa Rinpoche, Guru Devotion and His Holiness the Dalai Lama given at Munich, Germany in April 2001:
"It is important, therefore, at the beginning, before making a Dharma connection with a teacher, to analyze that person well. After thinking well, then establish a Dharma connection. The tantric teachings explain that in degenerate times such as these, it is difficult to find a teacher that has all the qualities as they are explained in the teachings. If that is so, still, your teacher should have eight of them, or five, or at least four. At least the teacher should possess the basic qualities that I mentioned before. This will help you avoid trouble in future, avoid creating very heavy negative karma, such as rising heresy, anger, many negative thoughts, and also, after having made a connection, giving up. Checking carefully will help you avoid all these dangers.
Then, I want to specify one extra point, on the basis of the usual examination that is explained in the teachings. I want to add that, if you are making a new Dharma connection with a teacher, you should examine to make sure that that teacher is not someone who is against His Holiness Dalai Lama with respect to the practice of what’s called döl-gyäl, the protector Shugden. Make sure that that person does not do the practice. These days, that’s an extra analysis you should make. In that way, you’ll avoid problems in future.
Recently, I also introduced a new guideline for the protection of the centers and their students, which is not to invite to the center teachers who do the protector practice and are therefore against His Holiness the Dalai Lama. "
It is this mixing of real Dharma from the scriptures and text with some "opinion" or political stands that confuses new Buddhists and non-Buddhists. I have never read in scriptures that we need to check whether the teacher is someone who is against the Dalai Lama, nor a teacher who does any particular practice. I have never read anything that explicitly state nor hint this in Gurupancashika (50 Verses of Guru Devotion) by Ashvagosha, The Fulfillment of All Hopes by Tsongkhapa, nor in the Mahayanasutralamkarakarika where Maitreya Buddha explained the ten qualities of a Mahayana guru.
Morever, in this degenerate age, it is already very difficult to find a teacher and study Dharma, now we have to even consider whether he practises Dorje Shugden. Isn't it better to practise with an "evil" Lama than not to practise at all? We are living in the degenerate age, hence any connection with Dharma is better than none?