What happens to port isolation in a Wilkinson power divider when source impedance isn't matched?
No, unfortunately the isolation is not maintained.

The reason you get very little signal at Port 3 from a Port 2 signal is that normally the amount of signal that goes through the 100 ohm resistor is about the same as the net amount of signal which comes back through both transmission lines.  About 2/3 of the signal goes through the the first line and about half of that (1/3 of the original) comes back through the other line.  These (approximately!) 1/3s are 180 degrees out of phase (two 90 degree lines) and cancel.  Of course there is a reflection at each junction and this only works out in steady state.

In any case, if the impedance at port 1 is not 50 ohms, more or less that 1/3 of the original signal will be transferred down line 2.  This will either not entirely cancel or over-cancel leading to a net signal out of port 3 which is based on the signal at port 2.