I totally understand what you're saying, and I kinda agree with you: games don't have to be fun, or to put fun at the center of their design. My take is that it's OK for some games to be focused around simple fun, and fun can have the "greater meanings" you're talking about: Minecraft is a good example of that, and I'm thinking of Tearaway, a game about paper made by the studio behind Little Big Planet, which explores the link between the player and the digital world in clever and unique ways, and it definitely has interesting things to say about creativity and how everybody can create. Fun can let players explore deep themes, it's just a particular lens to do so, and it isn't the best one for some subjects of course. In a way, the greatest meaning I can think of (for this specific kind of games I called joyful games) is if a game makes you want to share it with others, play with others and get to know others: putting people together is the best thing that these games can do, in my opinion.
On the other hand, I'm completely okay with games that aren't fun. I didn't know about Pathologic, but I have a few examples in mind of games that explore frustration, fear or disagreement between the player and the game in interesting ways (Papers Please comes is the first name I can think of). As for exploitative fun games, I hadn't thought about that: of course there are things to avoid, but as long as there's big loads of money to gain, some studios will take the manipulative path. Fortunately, for each of these games, there's a respectful game out there somewhere.
Another thing that comes to my mind: you talked about Pathologic as a game that let people argue, defend their opinions and, in some way, engage with each other; and I talked about how joyful games can aim to get people together. Isn't that the same goal? Would it be possible to say that, beyond fun or no fun, games have the power of connecting people, and they just take different paths to that?
I don't know, but it's such an interesting subject.