There IS a "kinda" workaround that you can employ that seems to work.
I'd only suggest it for singleplayer dynasties because it is really pretty "cheaty". You can temporarily **bleep** your players right before they make the decision on if they are going to declare or not by editing their stats.
Temporarily set a Wide Receiver's speed to 1 for example and then set it back to what it was before afterward. As you noticed, the magic number really does seem to be 90 overall player rating. Once a player is below that, they seem to be much more amenable to either not leaving at all, or at least you having the option to try and persuade them to stay.
Personally, I just think that EA needs to ease the throttle back on players leaving with no chance at all to persuade them. This seems like something that should be patched in some way. Either make the Program Builder Perks a lot stronger, or make the players much less likely to leave until after their JUNIOR year and not the SOPHMORE year.