One of the big points in that article mirrors your example. The correct response is to allow the user to decide.

"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas"

"This software program conflicts with this software program. You can choose to run them both and accept the problems that occur accordingly or you can choose to cancel this installation or remove program X"

Do you want to cancel, remove program X, or cancel the installation?

Give users the option to opt-into using your software, don't force users to get into a proxy battle by automatically opting into things.