I think Lama Zopa has not broken his samaya. From the outside, it may seems so because of FPMT banning the Protector's practice according the Dalai Lama's wishes, but from the inside, we can't be sure. I believe, Lama Zopa has strong Guru Devotion and the photo of Lama Yeshe in their centers proof it. Respect to the Guru form the basis of Guru Devotion. One can disagree with Guru and seek his blessing for this "disagreement" but more importantly, if the situation is such that many more will benefit, the Gurus will give their blessings. In these case, we are talking about 2 high Lamas. Hence, the workings of their minds may be beyond our comprehension.
On our side, we just need to respect all traditions and especially our Gurus.