Rav Hirsch demanded a clarification and asked for a cherem if Frankel wouldn’t comply. Rav Hirsch wasn’t so worried about his personal ideas. But what his students would feel their obligation to the future of klal yisroel. It’s a great insight and shows the clarity of Rav Hirsch’s vision. It could be used to contemplate the utility of any branch of Ortodoxy.
Just because Frankel could not see the future, it doesn’t mean he was less Orthodox. His theories of the Mishna stand and fall on their own merits.