Is it safe? 9v from 12 to 3.3 on ATX PSU
It depends on your 9V device and the load on the 3.3V line. You're essentially using the +3.3V to sink current from the 9V device. SMPS supplies can in fact sink current but only if they're designed to do that and plugging something into the output and hoping for the best will usually end up in tears. 

It may be OK if you have significant load on the +3.3V line exceeding the 9V device current. In this case the +3.3V regulator will simply supply less current and all is good. If this is not the case, +3.3V voltage will start to rise and trouble ensues.