Rav Schach said (it is quoted in the Introduction to Shorshei Minhag Ashkenaz, vol. 1) that in Vilna, on Chol HaMoed, everyone put Tefillin on with a Bracha, except in the Gaon’s Kloiz. Also, in the time of the Vilna Gaon, he was the only one to run a Minyan that did not put on Tefillin, despite the local custom.
If the Gra could flaunt the local custom with a separate Minyan, this shows that running a separate Minyan, is not in violation of Lo Sisgodedu and is permitted. Thus, one can run a Minyan for Tefillin wearers in Israel without reservation. And don’t say that the Gra was an extremely holy man and thus he is permitted things that we are not, because that is a Christian concept and has nothing to do with Judaism.