They've got a giant ECM strapped to their back that can make them invisible and temporarily disable enemy armor. I think it's appropriate that it should also screw up enemy targeting.
Unlike Guardians who can shield, and Strikers who can boost away, Recons really can't do anything once someone starts a toothpick combo on them.
You got it all. Auto-target honestly doesn't belong in PvP... but since it seems that suggestion isn't going to pull through any time soon. Just do this please? It'll make the recon class valid against these wolver-clone auto-targeting people. At this current point I'm better off going guardian with a giant flag sticking out my rear screaming "lookatmeimgoingforCP_!!!" than reconning and attempting a capture.