In the general case, yes, sometimes midrashim absolutely interpret pesukim which are in variance with the masoretic text, and which we can find in the Septuagint, or the Samaritan text, or the Dead Sea Scrolls. I've written about this extensively, and linked is one such example.
So, it is not impossible that Rabbi Avin bar Kahana (a third/fourth generation Amora of Eretz Yisrael) had an alternative text before him. Supporting this read is that the midrash, in the version as we have it, seems to take the Biblical phrase and interpret it. So תּוֹרָה חֲדָשָׁה coming from Hashem is interpreted not as a new Torah supplanting the old, but as חִדּוּשׁ תּוֹרָה, an innovation within Torah.
However, while variants certainly crept into the Biblical text, there was an internal process by which scribes attempted to maintain the integrity of the Biblical text. There were codices such as the one kept in the Temple Courtyard, and later the Leningrad and Aleppo Codex, and others. This is not the case for the text of gemaras, midrashim, and so on. If so, the error could also plausibly be in the midrashic text, rather than in the verse it quotes. Especially since we don't know of any extant variant text of Yeshaya (I checked Vetus Testamentum) that has this change, and we don't even see this in Christian translations, where they have all the reason to maintain this variant.
Indeed, in the Beur Maharif on Vayikra Rabba, by Rabbi Yechezkel Feivel, the Maggid of Vilna, he asserts that the midrashic text is erroneous and that the correct text doesn't have חֲדָשָׁה in the Biblical citation. I have not checked variant manuscripts of the midrash, and I don't know if he based himself on logic (that that isn't the Biblical text) or on some extant manuscript of the midrash.
If the word חֲדָשָׁה isn't present in the citation within the midrash, the interpretation still can work. The derasha is based on the word תֵצֵא in the imperfect (that is, future) tense. With that, the verse implies that Torah comes forth from Hashem in the future. This is thus a new Torah. And Rabbi Avin b. Kahana essentially says that this refers to innovations in Torah.