Well, out of my experience on hslan, allowing attacking on crossed flags, has no negative impact on gameplay. Sometimes some people might attack uncap flags, yes, but that basically just makes it easier for defending side, as some of attackers are wasting their time at uncap.
About spawn rape, I have never even warned anyone about spawnrape on uncap flag. I'm not saying it could not happen, but it's rare and relatively small problem, because afterall it is uncap and defending side won't probably spawn there because they have no need to defend it. On top of that, every flag has several spawn points, so chances are, that if you get killed on one, you likely just spawn on other point and go kill that camper.