In recent times, it is noted that the impact factor is widely varied in the journals under the fields of Physics, Chemistry, Materials science, Biotechnology etc. It does not mean the journal with high impact is high quality in comparison to the journal with low impact factor. The journal with high impact factor in Biology or chemistry may be of high quality among that category, but cannot of comparable of other category journal, e.g., in Physics, as the scope and quality of presentation is largely different from the scope and presentation in chemistry or biology journals.
There are different ways to measure impact factors of journals, so first you need to be clear about which measure you mean. For most there is some attempt to normalize based on the # of citations relative to # of publications, but this has many flaws. So yes there will be much variation in the impact factor of the top journal in one discipline relative to another discipline based on the size of that discipline (how many researchers, how often they publish, and what is the norm with regard to citing other's work). In short, there is not a simple answer or solution to your question.
Summarizing the views of Benedik and Farid, I think it is possible to adopt a standard procedure for normalization of impact factor in journals belonging to different fields. Yes, there are various factors to be taken into account and that also could be a matter of debate. However, certainly the number of articles published per year could be one of the factors to be taken into account, in addition to how many average citation per paper per year in that journal.
Actually that is not what I was trying to say. While publishers do try to normalize based on the number of publications in the journal, that does NOT standardize across different disciplines. I don't believe there is any simple metric that you can use to rank "equivalence" in terms of stature of journals in different fields.
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