As i see it if it is a positive ground would plugging the lead to the amp that is grounded just short the 9v supply straight to ground.
Don't think of it as if you're shorting out the battery. All you're doing when you plug in is to connect the + battery to ground, just as if you had turned on a switch.
You can't just flip the ground system between positive or negative by changing from PNP to NPN. There are other considerations too. You must look at the schematic and determine if you need to reverse the polarity of any electrolytics and diodes.
There's nothing wrong with using a positive ground. Most of my pedals use positive ground. Just stick to your original circuit and transistor type and find the problem (most likely a wiring error or transistors not connected properly).
If you have switched battery polarity with transistors in circuit, it's likely that the transistors are now shot.