You are correct, those are serious issues facing jobs that use the zones with pullback protection. We have a couple of Standard Operating Procedures when using RCO that ostensibly minimize those risks:
-The first thing you do after linking up and going through your safety checks on the locomotive is acquire the zone you will be using from the yardmaster. Like a prized possesion, the zone is yours for the duration of the shift and you are the ONLY one who can allow anyone else to occupy it. You release it at the end of your shift to the next crew, or it becomes inactive and the yardmaster can use it as he sees fit.
-After you've established your zone, you run light power to the end of it. This is where you're looking for misaligned switches, track defects, derails, etc. You're also testing the pullback protection. Once you've gone out and back and your zone is how you need it, you can start work.
The big problem this DOESN'T address is the danger of hitting tresspassers on the ROW. Out here in Portland on the UP, they spent millions of dollars eliminating grade crossings and posting those bright yellow "Remote Control Operation In Effect-Locomotive Cabs May Be Unoccupied" signs. Their view is that people shouldn't be walking on the tracks and they've done everything they can to protect the public. I don't worry so much about hitting a transient or other adult who knows better, but I always think about kids walking along the tracks. Very sobering.
Overall, the RCO incidents we've had out here (many more than you'll hear reported) have had almost nothing to do with unmanned pullback operations, the system works like it should. All our problems come from crews taking shortcuts, not protecting the point on shoves and running through switches/into equipment and general inexperience (of which I'm guilty of myself at 7 months on the job). Honestly, everyone here has their fingers crossed that these things will eventually go away with all the equipment problems and incidents we've had. However, from the amount of money UP has spent to implement RCO, it's probably not realistic to think that they will go back to conventional jobs with engineers.