I think USAF and other companies were likely part of the reason Sony removed Linux support. Generally, a PS3 was a lot cheaper than the equivalent PC/server.

Sony typically sells consoles at a loss and makes profits from the game sales. The likes of USAF, researchers, and other companies were buying PS3s in bulk, and using OtherOS functionality without utilizing the primary use of PS3s: games. Often these projects didn't need any GPU power, and OtherOS had nearly full access to the CPU (iirc it had access to the main PPE and 7 out of 8 SPEs). Thus, Sony likely was not making enough money from the consoles USAF et al. bought.