The question is, why was he excommunicated? It couldn't have been just for expressing his opinion, since the Mishnah is full of dissenting minority opinions. Was there something special about the nature of this dispute that warranted this sentence?
At the simplest level, he was acting in a manner akin to the zaken mamre or "rebellious elder" (Deuteronomy 17:12). As the Gemara in Sanhedrin explains, a member of the Sanhedrin is allowed, and encouraged, to express a dissenting opinion. However, once the Sanhedrin votes and his opinion is determined to be the minority, he may still:
He may not:
Rabbi Eliezer wasn't excommunicated for saying "I think the oven is tahor", he was excommunicated because he couldn't acknowledge that he was outvoted here, and would have insisted on continuing to practically tell anyone who asked him that the oven is tahor. The oven happened to be what brought up the broader question of the halachic process. Keep in mind this was a tumultuous period in Jewish history, with all sorts of splinter groups and a great deal of confusion after the Second Temple was destroyed. Rabbinic Judaism was spared the split that you'd see between, say, Shiite and Sunni Islam, because minority views were acknowledged (and respected) but then for our faith to remain cohesive we picked the majority view and went on from there.
Personally I find this reading strong enough as is.
However, Rabbi Yosef Eliyahu Henkin z'l did in fact feel that this "oven" discussion was code for something larger, i.e.:
His grandson, Rabbi Yehuda Herzl Hekin shlit'a, questions this interpretation as conventional history has Raban Gamliel (and the general majority) accepting Roman rule, with those who would take arms (e.g. Bar Kochba) to be in the minority. Rabbi YH Henkin therefore suggests a slightly different interpretation. He starts by observing Rabbi Eliezer's opinion in Pesachim 9:2: if you are one step outside the Temple, halacha deems you "on a distant path." We therefore have:
This works nicely as we follow Raban Gamliel's more forgiving opinion. (Similar to R' Tzadok HaKohen's interpretation of the hagada's response to the wicked son: "the time for filtering out the Jewish population was the Exodus. But guess what? You were redeemed. So you're a part of us now, whether you identify with it or not.")
(Rabbi YH Henkin's interpretation, and that of his grandfather, are found on an mp3 of his on yutorah.org)