While it's their choice, it's shooting themselves in the foot. Just like Nintendo's requirement that to make a downloadable Wii (U) game you need to have a physical office.
Indie sales still generate legal tender.
But is anyone buying a new GPU so they can play an indie game? I think Mantle is more about getting benchmarks of Call of Duty online showing that AMD hardware is faster than the non-Mantle NVidia hardware it's compared against. Nobody does benchmarks of those indie games, and no one looks for them to base their purchases of hardware of them either. The indie games are likely to stick with OpenGL anyway, since they have to support that for other hardware and don't have the resources to maintain a bunch of different optional backends.
While an indie game alone won't sway anyone's purchase decision, it's still positive PR for both AMD and that game. AMD gets to claim "X more games support Mantle", game gets free publicity for being mentioned in AMD press releases. It should be a win-win situation.