I agree, many may not agree with the "middle way" that Tsem Rinpoche is promoting. But coming to think of it, what he is promoting makes sense as well. When we say that H.H Dalai Lama is the false incarnation, it will not be correct as well. What if the current Dalai Lama is a true incarnation? By us calling him as a false Dalai Lama, we create negative speech karma.
Ling Rinpoche and Trijang Rinpoche would know that the current incarnation is not the true incarnation if H.H Dalai Lama is not the true incarnation. How could these two great masters be his tutors and not know the truth?
With that being said, I also believe that H.H Dalai Lama is putting a ban on Dorje Shugden for a greater reason. At the same time, it is because of this ban, many people know who Dorje Shugden is. It might be that H.H Dalai Lama is using this "stunt" to make the practice bigger.
Only time will tell. We have to persevere and push on with our practices despite what is going on. As long as that we know what we are doing is correct and we are not breaking our samaya, it will be fine.