I think you are too concerned with micro optimizations.  get-in is probably 
just as efficient as attempting to bubble the state change back up and 
certainly simpler to work with.  In practice, optimizations like this do not 
have a significant impact on the overall performace.  
Measure before you optimize.  I might also add, parrelize before you optimize. 
Immutable data structures often makes it much easier to parrelize the 
algorithm, so even if you do have slow spots if the applications critical path 
is not affected you still may not need to optimize. 

There probably are several methods in clojure that can be significantly 
optimized and eventually someone will, but the best optimizations will come 
from real world performance problems not theoretical ones.  Do some research on 
clojures vector implementation and you'll see the fastest implementation in 
theory is comparitively slow in practice due to the way the caching works. 

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