Sticking with the premise that the entire 'machine' needs disposing of.
If deaths of AI are rare, and even rarer still in the case of Building AIs. Why do anything at all? It would make perfect sense (due to the impracticality of any other option) to simply let the building stand as a monument to itself.
It would be 'made safe' as sensitively as possible, which would be analogous to embalming, possibly assigned a warder/guardian/curator, and left empty for the rest of time.
Ships are easier to deal with, they could be given either a Viking burial (perhaps via atmospheric re-entry, or directed at a star,) or simply 'Buried at Sea' (cast adrift, possibly targeted at some 'special' uninhabitable region of space)
I think you could have a good reason to do this (to explain why they're not just recycled) if the AI ships and buildings were said to be self-assembling to some extent. Their mind and body built in an 'organic' process where they develop in parallel. There is no way of distinguishing where the 'mind' ends and the 'machine' starts.