I think this was a horrible decision by the Eagles front office in every way, but I don't think it will scare off free agents. They've messed over guys in similar ways before, but when your contract has the biggest guaranteed dollar figure, it usually wins. Players are worried about a career-ending injury as opposed to whether they will be docked some cash for an illness and miss a few games, IMO.
Again, I'm not defending the move at all. I just don't believe it will prevent them from signing free agents...they are mercenaries who invariably end up going to the highest bidder.
I think it hurts them more with their own guys. Let's say, for example, Fletcher Cox has watched Patterson go through brain surgery and fight to get back on the field. He's heard Cole and some of the older guys talk about what a great guy he is. They know he's the longest tenured player on the roster...he's been in Philly longer than anyone else, he's never played anywhere else, and he's never complained about anything. Patterson catches a cold and being the guy he is, works hard every day even though he feels like crap. In the process of playing through it, he made it worse and the end result was pneumonia. The Eagles respond by docking his pay.
Now, what's Fletcher Cox (or anyone...just pulled his name out of a hat) thinking? When he doesn't feel 100%, is he going to take his foot off the pedal a little bit? If he's dinged up and doesn't feel great, but he thinks he can help the team on the field with what he has left, maybe he decides it's better to play it safe rather than risk it. Maybe in a blowout game or down season, he thinks it's best to mail it in and stay healthy.
You have to expect 100% out of your players, but the players have to feel like the team will take care of them. If their body simply breaks down, gets old, they don't put forth effort, or whatever...fine. Tough choices have to be made. What is the message the Eagles are sending to the locker room with this move? Do you think they feel like they are taken care of? That the organization has their backs or cares about them? Should they push through the pain or protect themselves? It might not impact them at all, but I can't say for sure. I'd much rather build some goodwill and take care of a team guy rather than go out of my way to assess a petty and insignificant (to the team) penalty for an illness before handing it over to the lawyers.