I understand your concerns, but you already let the cat out of the bag. If they are going to use the patched versions, then how is discontinuing the feature going to stop them? They'll just do what I have to do know, use an older version. Seems to me that you are just hurting the people that are using it legally, not stopping anything.
As for the AV companies, let them stop the patched versions. As they should. They should only be whitelisting the legitimate version's signature. All other variants should be considered as unsafe. It's not your problem/fault that someone else is hacking your application. If the AV companies banned every application that was hacked, then no Microsoft app would ever pass their tests. Especially since MS products have been used as an attack vector since the beginning. Let the AV company do their job and block the proper signatures instead of just blacklisting your app. Seems like laziness on their part.
Ultimately, this is your call, but if we removed a feature from an application every time someone has an issue with it, we wouldn't have any applications. Someone always has an issue with something, even if it's legitimate or the mass likes it.
I'm really disappointed that you are removing a very useful feature. I hope you reconsider. You really shouldn't let other companies dictated how you design your product. You should listen to your users and base your decisions on their input. They are what matters, not other companies. The AV companies have no say and should do their job and filter the hacked versions, not the legitimate one.
I just updated to the latest version hoping for performance boosts and I find out that you removed one of the most useful features for me (I use many of them). I see an older post from September saying you were discontinuing this feature. Why? It can't be privacy concerns since you have the banner displaying while it's active.