They can't encourage them overtly without damaging their relationship with the music and film cartels -- without which they lose the most successful commercial music market on the internet. And the MPAA, RIAA and their members hate the idea of uncontrolled access to machines that host their media. (EDIT: Also, the cellcos presumably don't like the idea of uncontrolled smart devices talking to their base stations ... as witness the periodic crackdowns on un-authorized tethering.)

But on the other hand, jailbreaking isn't impossible. And it ought to be -- if Apple seriously wanted to design a machine that couldn't be jailbroken, then some combination of a trusted platform module with remote activation (which Apple indeed enforce) should be sufficient. (Kernel isn't signed by Apple corporate? Boot loader say bye-bye!)

So my conclusion is that Apple are doing "due diligence" -- enough to propitiate the copyright absolutists, but dragging their heels enough to permit a deniable halo of JB developers to generate new ideas, which can then be bought in-house if they work or disowned if they don't.