my bitcoind seemed to handle it just fine
~$ grep -i '000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881' .bitcoin/debug.log
received block 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
REORGANIZE: Connect 2 blocks; ..000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
SetBestChain: new best=000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881 height=249673 log2_work=70.984974 tx=21401321 date=2013-08-01 19:25:08 progress=0.999998
received getdata for: filtered block 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
received getdata for: filtered block 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
received getdata for: filtered block 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
getblocks 249672 to 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881 limit 500
getblocks stopping at 249673 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
getblocks 249672 to 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881 limit 500
getblocks stopping at 249673 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
getblocks 249672 to 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881 limit 500
getblocks stopping at 249673 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
getblocks 249657 to 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881 limit 500
getblocks stopping at 249673 000000000000003d83ba9beb36d3642df1165bd070abc74aacd180262b595881
although I can't find "ERROR: mempool transaction missing input" in my logs.