You have a brand that requires trust. You've built up that trust slowly, and it could be destroyed so easily. To me this injection crosses a line of interfering with content that isn't yours. You are trusted to have access to this content, not to change/add to it. I get that it's not quite the same as 3rd party ads, etc. But it's an untrustworthy thing to have done.
As a happy long time user I'm currently still willing to give some benefit of the doubt about this being a misstep, and I'm hoping to see it corrected shortly.
But I think the value of the trust you've built up shouldn't be understated. It won't take many scandals like this and once the trust fades you'll never get it back. The bigger issue to address is not just how to fix this, but also how to fix the broken decision making process that allowed this to happen at all.
Someone else has said about having a core set of values against which everything is reviewed. How about an ethics committee of sorts to uphold those values. A group of beta tester users who don't just test things work, but also give feedback on whether new changes are aligned with your brand and core user base. (Email is in my profile if you want to discuss this idea, if be interested in helping)