zsousa,
How do you execute the tests?
Like KarelHusa suggested, there is command line option if the tests are run using SOAPUI_HOME/bin/testrunner utility which does not save the project after tests are done.
But if the tests are being executed using UI, then you may not have that luxury.
And it is understandable the pain of this differences while working with repositories like git / svn/ cvs etc.,
Anyways, it is possible to either clean the property values or remove them altogether easily by writing script and keep it at Project level "Save Script". That is, as soon as the project is saved, all the properties are cleaned or removed amazingly in a second.
However, caveat is that it may clear certain properties which you not intended to clear for a test case. Of course, that can be handled by having a list of property names that can be excluded and filter them while clearing.
And there is another issue is that whenever the project is saved, the properties are cleaned which again you may not want to do so or annoying at times. Again clean of these properties can be done conditionally so that there is better control whether to run whole Save Script or not.