There will still be some conformation changes following the zymography protocol. For example a proenzyme may show activity not occurring in vivo. However, if you are comparing the same enzyme on the same gel from two different tissue treatmentsq, and normalize the sample amounts, you can compare relative activity. I used amount of DNA as an indicator of cell numbers in loading zymograms. This shows relative amount of activity/amount of an enzyme under different conditions, not changes is biochemical properties of a particular enzyme.

If you will use equal volumes of samples on the same gel in the same conditions and normalize the amount of protein into all samples then you can compare the activity. It will be relative actitvties. But if you will put also standard mix of enzymes with known activity on the same gel then you can calculate the actual activity relative to standard proteases mix.

It is also worth noting that zymography can show you the ratio of active-enzyme:pro-enzyme which may be more important with respect to determining the amount of biologically relevant enzymatic activity