At FOSDEM this year there was a very good presentation by Robert McLay of TACC 
on XALT, which tracks how
supercomputers are being used down to the level of binaries and libraries:

https://fosdem.org/2016/schedule/event/hpc_bigdata_xalt/

https://fosdem.org/2016/schedule/event/hpc_bigdata_xalt/attachments/slides/1189/export/events/attachments/hpc_bigdata_xalt/slides/1189/xalt.pdf

https://www.tacc.utexas.edu/research-development/tacc-projects/xalt

They use LD_PRELOAD to link in a bit of code which runs at the start of every 
job.
I don't think they do exactly what you want - ie to look at opcodes. But you 
could do worse than contact them and see if this approach could
be useful to you.
I guess though that they are recording what binaries and libraries are used  - 
ie the job is always  started.
You are aiming to analyse a binary and to prevent it running on the wrong 
architecture.
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