I agree with WOWMom. I don't think med schools would care enough about this certificate to look past a lower GPA. Some things to consider:
1) Why do you think these classes would lower your GPA?
2) If the classes sounds interesting to you, and you have limited time (ie only until you graduate) to take interesting classes just to take them, is that worth the potential GPA ding?
3) Are there other potential benefits to these classes? Intangible things, like getting to work with awesome professors? More tangible things, like exposure to different fields you might want to do research in?
4) Could you accomplish your goal of learning about the conceptual foundations of medicine by choosing, say, some of those courses, and not actually getting the certificate? Does having the certificate add anything beyond just having it?
If I had a good reason to believe these classes are just going to be GPA busters, I probably wouldn't take them solely to get the certificate--but I might take them because I'm interested in the material. If I've heard the class is hard but don't have any real reason to believe it'd be impossible to get a good grade (B+ or better), I'd probably take it. If I had reason to believe there were other things to gain--such as taking a class from a great prof or gaining exposure to a new field to do research in--then I'd probably be more willing to sacrifice a little GPA to get there. Obviously a 3.98 is awesome, and luckily for you, there's probably a little wiggle room there (meaning you could "afford" to get a B or 2 if, in exchange, you get some awesome experiences out of it).
Just my opinion though.
(Then again, as an undergrad, I sought out the most challenging versions of the classes I wanted to take, and I stumbled upon a kind of random minor in leadership & public service based on a variety of classes I coincidentally took.)