The marketing value of a supercomputer built from your company's product is surely worth the loss of subsidy. Each time one of them is built, it invariably results in a bunch of news stories. This helps reinforce the PS3's reputation as the most powerful modern console hardware.
They're probably enabling it in some cases -- the US military has built clusters with thousands of PS3s. I doubt they procured those through Best Buy.
Even if it's not, Sony could have sold unlocked* units at a non-lossmaking value, which would have instantly discouraged a large proportion of the hacking movement. This is what OtherOS provided: a valve for homebrew enthusiasts, why there were no serious efforts for the duration.
*By unlocked I mean "homebrew unlocked" and without the ability to play games.
They're probably enabling it in some cases -- the US military has built clusters with thousands of PS3s. I doubt they procured those through Best Buy.