R. Yeshaya of Trani (the Rid) applies אלו ואלו to the post-talmudic period in a responsum (Teshuvos HaRid 62).
As cited and translated by R. Shnayer Leiman here:
First, I wish to respond to your claim that it was improper for me to argue against the great Rabbi Isaac lb. Samuel of Dampierre (d. circa 1185)), Heaven forbid that I should do such a thing! It never entered my mind that I was arguing against him. I am but a single flea (I Samuel 24:151) i.e., an ignoramus-so Targum Jonathan renders the phrase-in comparison to his students, how much more so when I am compared to him! But it is my practice to dismiss all opinions that appear to me to be mistaken. Should Joshua the son of Nun endorse a mistaken position, I would reject it out of hand. I do not hesitate to express my opinion, regarding such matters [...] we are dwarfs astride the shoulders of giants. We master their wisdom and move beyond it. Due to their wisdom we grow wise and are able to say all that we say, but not because we are greater than they." Furthermore, we wish to state that we have confined all our arguments against opinions expressed by the rabbis who preceded us, to those instances where they themselves disagreed, the one permitting, the other prohibiting. Now how shall we resolve such a dispute? Can mountains and hills be weighed on scales? Can we decide that one rabbi was greater than the other, and then discount the opinion of the lesser rabbi? We have no choice but to examine their opinions-all their words are the words of the living God-and then decide which one accords best with all the evidence and merits becoming authoritative.
The original text of the responsum is available on HebrewBooks here.
Similarly, the Rivash (14th cent.) describes in his responsa (ch. 505) the contemporary dispute over the recitation of the "shehecheyanu" blessing on the second night of Rosh Hashana as "Elu V'elu".
אומרים זמן בליל שניה של ר"ה; והאומר: שלא לאמרו; אלו ואלו דברי אלהים חיים. שכבר נחלקו בו הראשונים; זה אומר בכה, וזה אומר בכה.
It should be noted, however, that it is possible (in my opinion likely) that they uses this as a mere expression to refer to the greatness and legitimacy of all parties involved; not as reference to a particular philosophical status.
Additionally, R. Moshe Soloveitchik writes explicitly (as cited in Kol Brisk) that אלו ואלו applies to Rishonim. He seems to be using this as more than just an expression.