Wow, tons of action on this thread! I really appreciate all the comments and advice. I decided to not argue with them about the engine replacement because I didn't think they would be open to taking the vehicle back. If anyone has experienced, or knows anyone who experienced a dealer taking a car back because something doesn't sound right in it, let me know because I could have that in my back pocket if I'm not happy.
A few things make me think getting them to buy it back without allowing them attempting to fix it is practically impossible. For one, there are no drivability issues. It just makes a noise. I don't know what damage it's causing to the engine, and I don't think Ford knows either, so they're eliminating all the possibilities with a new engine. That could be because they only have 3 attempts to get it right before they're stuck with a lemon and a loss. Maybe their engineering department wants to tear it down and see if there's something specific about the problem that could be related to the ST. If they did buy it back, they would have to replace the engine and could only sell it as a use car because it was titled. Swapping the engine in this short a time seems to be the best way to get the customer on the road with the least hassle possible.
Personally, I'm happy I don't have any inconveniences. Even if they screw it up trying to get the engine in, they have to make it right or I won't accept it. No, there are no guarantees that things are going to be perfect, as it was when I had to have the entire driveline, axle, rear and suspension removed to replace a clutch slave cylinder in my 97 Vette. But, it drives just fine. As long as I'm happy with what I get back, I'll gladly give them their new Explorer back. If they can't make it right, I'll put the miles on the loaner until they can get it right, all the time complaining to Ford customer assurance.