I concur with akuperma’s points above, except that Lipman pointed out that his goal was that they be funded independently AS SOME SCHOOLS ALREADY ARE, not that they be closed down.
Regardless, were it not for the Zionist factor and other factors, as Rabbi Yonasan Rosenblum described in his piece titled, “Where the American and Israeli Torah Communities Differ”, my guess is that Rav Feldman’s reaction would have been different.
So it seems that there are some minor issues with Rabbi Lipman’s position; whereas with arguably greater issues, like Zionism, for example, I don’t see everyone rushing to similarly condemn Rabbi Kook and his followers the same way, despite similar denigrations being heaped on them and/or their “shitos” by one or more gedolim and the reality proving those “shitos” to be wrong.