1) The story about Rashi's daughters wearing tefillin is an urban legend. (See this article in the Jewish Action: What’s the Truth About…Rashi’s Daughters?)
2) What about Michal bas Kushis (or Michal bas Shaul)? She wore tefillin, after all! This is also the stuff of legend. Be honest, you non-chareidim. Do you think (a) that the historical Michal daughter of Shaul really wore tefillin and this is an oral history, or (b) do you think that it is a midrash which some rabbinic figure came up with, perhaps by close reading of some Biblical passage, and perhaps to teach some important lesson? When the gemara says that she wore them ולא מיחו בידן חכמים, the Sages did not protest, do you think that historically the Sages were around to protest or not protest?
Such a tenuous fable was not sufficient in Talmudic times to arrive at a definite halachic conclusion. Rather, the rabbis interpreted the halacha in light of the halachic system they had assembled before them.
That is what the Yerushalmi is doing in Eruvin 59a:
התיבון הרי מיכל בת שאול היתה לובשת תפילין אשת יונה היתה עולה לרגל ולא מיחו בידם חכמים. רבי חזקיה בשם רבי אבהו אשתו של יונה היא שבה מיכל בת שאול מיחו בה חכמים.
That is, Rabbi Abahu holds that (certain) instances of petur from tefillin also establish an issur to wear tefillin. Thus wearing tefillin at night, a time of petur, is also forbidden. And thus a woman wearing tefillin is forbidden. They object from this midrash, and they cavalierly rewrite the midrash. How do you know the Sages didn't object?! Since we know it is forbidden, say they objected.
But really, that is not the way halacha is established. Just like we don't establish women as dayanim on the basis of (misinterpreting) a pasuk about Devorah being a "shofetet" or women as mohalot on the basis of Tzipporah, in an emergency situation before mattan Torah circumcising her son. (Gemaras and Tosafot notwithstanding.)
3) Even if there is halachic basis for an action (at the same time that there is solid halachic precedent against the action), that does not mean that every praiseworthy action should be taken.
No, this is not (entirely) impugning the motives of women wearing tefillin, in a way that we do not subject men to such scrutiny when they accept some extra practice.
Rather, it is recognizing that historically, praiseworthy actions have been abandoned by the Jewish people in the face of outside groups co-opting it.
If I got up in shul and tried to establish that they publicly recite the Aseres Hadibros every day, people would object, I think / hope. Even though this was the practice in the Beis Hamikdash. Why? מפני תרעומת המינים. Rambam objected to standing up specifically when the Aseres Hadibros was read (though this is admittedly and unfortunately current practice).
They used to decorate shuls with foliage for Shavuot (and still do in my shteible), but the Vilna Gaon tried to get it nullified when Christians had a similar practice, and many shuls no longer do it.
Even though the avos offered sacrifices of matzeivos, because pagans did so, this practice was later Biblically rejected.
Certain actions which otherwise would not have been considered optimal were taken להוציא מלבן של צדוקים.
And like it or not, there are other current sects of Judaism which, in the interests of egalitarianism (and which believes that Orthodox Judaism has been treating women unfairly and unequally) has established the practice of women wearing tefillin.
If so, it is not a simple appeal to rare historical precedent or finding classical sources which permit or encourage it. Rashi's daughters, had they worn tefillin, did not do so when there was a competing sect promoting the wearing of tefillin. So too for Michal bat Shaul. So too the Rashba. Were the Rashba alive today, he would not just read the dry texts, but also realize that the same act hundreds of years ago does not have the same meaning as it has today, and he could very likely forbid.
Again, this is not to judge the motivations of the specific identified individuals involved. But the actual facts on the ground legitimately brings in the question of sectarianism, and maybe even a call to question motives in general.