I found a solution for the problem:
Use ValidMeasure() Function like this:
<Calculated Member: [Virtual Measure "Cube 1 Measure 1"] / ValidMeasure([Virtual Measure "Cube 2 Measure 2"])>
The Valid Measure Function will tell Mondrian, that this Measure has non-joining dimensions which can be ignored. Measure 2 will get joined against other applied dimensions and a value will be obtained, which then can be used for the calculation.