Wanted to recommend it and provide an Amazon link, and Amazon is all “that’ll be $124 new! Or $284.77 for the boxed set!” and that gave me pause.
In short, yes, it’s out of print. Supposedly there is going to be a reprint Really Soon Now, but most of the people here are not holding their breath. See this thread for more.
You can buy it in PDF from the usual places:
And the extra stuff in the boxed set: http://rpg.drivethrustuff.com/product/96735/Mouse-Guard-RPG-New-Rules-New-Missions