I think R Hirsh’s disagreement w/ scientific (Wissenschaft) method is not just w/ Frankel but also with other Orthodox school of R Ezriel Hildesheimer. R Hildesheimer though also considered Frenkel treif, so you may want to analyze their differences to understand Frankel positioning.
And even further, it seems that later German sources – R Weinberg – quote Frankel with more respect, maybe because there is less urgency in the machlokes. So, it may be true that at the same time, Frankel initiated a movement that let people astray, and have some valid points to make.
Why is this important? Maybe because we should not through babies into the mikvah: just because someone disagreeable mentions an idea, does not always mean that the idea is wrong.