And to answer my own question, the answer is to change the symbol to this:
var symbol = new esri.symbol.SimpleFillSymbol(esri.symbol.SimpleFillSymbol.STYLE_NULL, new esri.symbol.SimpleLineSymbol(esri.symbol.SimpleLineSymbol.STYLE_SOLID, new dojo.Color([98,194,204]), 2), new dojo.Color([98,194,204,0.5]));
Basically, a no fill allows the popup to come through...
Onwards to the next issue!