That is a good point. That is why some appliances are given a "hipot" test, or an insulation breakdown test. They should also be checked for good ground integrity by using a bit of current, perhaps 1 to 10 amps, and check for negligible voltage drop.
With isolation transformers, it is important to remember that there is almost always some capacitance from the primary to the secondary (and core), and thus some current can flow with AC applied, and a circuit (=path) to ground on the isolated secondary side. This can be minimized by using split coil bobbins or electrostatic shields, and of course the core and frame of an isolation transformer should always be well grounded.
There was quite a discussion a while back (probably on SED), about safe voltages and how much current is required for electrocution. It is in fact highly variable and depends on many factors. 50 and 60 Hz AC is unfortunately just about "perfect" for causing heart fibrillation, and apparently it doesn't take more than a few mA if the path goes through the heart. So a shock received from one hand to the other is likely more dangerous than one from a hand to a foot. But that is another discussion...
Be safe,
Paul