Note that in its present form, this blessing does not seem to target Messianic Jewish believers (the key word lamalshinim is normally rendered "for the slanderers"). But the Talmud (B'rakhot 28b-29a) states that the original form of this blessing had the term laminim, which is rendered "for the sectarians," which was generally understood to be the Essenes and Messianic Jews of that time. "If the chazan makes a mistake in any other of the blessings they do not remove him, but if he makes a mistake when saying the Birkat HaMinim they remove him because he is suspected of being a min himself" (B'rakhot 28b).
In short, the "blessing" was used as a sort of litmus test by the Rabbinics: a Messianic Jew could faithfully recite the other eighteen blessings of the Amidah but could hardly invoke a curse on followers of Yeshua the Mashiach. In this way, persons not reciting the Birkat HaMinim were suspected of heresy and subject to cherem (excommunication).