If my circuit is electrically isolated, do i have to worry about a polarizing effect on my sensor's output?
As the article you linked says, the signal should be "with a symmetric oscillation with respect to both electrodes (no net polarization)". Net polarization — an average DC voltage — will result in galvanic corrosion. Ensuring the average is zero means the corrosion reverses course perpetually and the electrodes will remain mostly intact.

Your proposed square wave has a positive average. Your isolated power supply is helpful because it ensures no current will flow between the sensor and anything else, but the sensor still needs to be symmetric.

In order to make a symmetric output,  use an H-bridge circuit to reverse the two electrodes. H bridges are commonly used for motor reversing and can be made of transistors or obtained as a single IC. Instead of generating a square wave signal that goes to an electrode, you would send it to the H-bridge to trigger the reversing.

Another way to make a guaranteed symmetric and isolated output is to use a transformer (at which point you don't need an isolated DC-DC either) but I don't know what effect that would have on conductivity sensing.