You've met the "due diligence" requirements by advising site management of your concern. You are not obligated to take it further.
In some companies, it may be considered appropriate to take such questions up the chain, either directly or via whatever indirect mechanism the company provides. But it shouldn't be done lightly. Remember that branding guidelines are just that, guidelines, and it's possible site management already has approval from Corporate for the deviation from standard practice... and that if you've been an outspoken critic, you're likely to be suspect as the source of the complaint even if there's an "anonymous suggestion" system in place. And it shouldn't be done contentiously; phrase it as a question rather than an accusation. ("I don't quite understand how this squares with policy, and I'd like to so I can do my job better in the future. Who should I talk to for additional education in this area?") That raises the issue without coming across as a backstab.
If you really think the decision is going to actively damage the trademark protection or otherwise cost the company a huge amount, and are willing to risk betting your job on either being right or being respected for the effort, that's one thing. (I might risk it in my company, for example, if this was an issue in my area of expertise and I thought megabucks were at risk; IBM has a pretty decent history in that regard.)
If not, then pick your battles. Remember that if it is a problem, someone from Corporate and/or the legal department will eventually notice it and decide whether something has to be done about it... and the blame, if any, isn't going to land on you.
(If this was a serious corporate ethics issue, I'd say take it up the chain and damn the torpedoes. But even then I'd phrase no more strongly than "this worries me, but I may be misinterpreting what I'm seeing.")