I find this to be a major issue with my moving through the campaign too. For instance, on one of the A10 missions, it says to go for the center 80's. I find them on the ground, but before I do that, my auto-targeting locks onto the sam quad located about half a world away. For some reason, I am unable to release my target lock.. AHHH! After taking those out with guns, the next auto-target locks onto the fuel truck, then the truck, then ANOTHER sam site, further away.
After I take those out, I go back to my original target (the 80's) and take them out (with my 65's). Now, I go back to the base, land ok.. and guess what, my wingman didn't make it. I watched the replay from behind my winger and guess what he did.. he skidded across the runway and hit a building.. and yes, he blew himself up.
I have found out, its better to tell my wingman to run trail formation, because otherwise, all he does is get himself in trouble.
Real quick question regarding sam sites... If I take the radar out (usually in the middle of the site), does that not render the sam site inoperative?