Wouldn't, possibly, it work better if the queue just wouldn't pop during a PvP match?
Allow people to queue for PvP while waiting for some other mission, but just not give them the option to queue out of a PvP match once it starts?
That way the people would have the option of PvPing to keep busy. If they lose their place in line in a queue for a flashpoint then so be it, but if the flashpoint was slow coming together, it might still be waiting for them when they get out of their warzone, particularly if they were a tank or a healer.
Think about it though... in the context of our player base. Wouldn't that generate as many complaints though? Along the lines of "OMG.... I never get a flashpoint queue pop!!!!.....SWTOR is Fail!!.... Fix it NAO!!!!"
Personally, I agree with their change to the mechanics here. Fact is, if people would show some self-discipline and not drop from group when something better (to them) pops, they would never of had an issue to address here. If you join a group to do something as a group.. you should show commitment to the group to finish what you started IMO.... not just run as soon as the candy bell goes off. Since people can't self-discipline, Bioware did it for you.