The old version does AVX and the new version doesn't? Thats crazy! AVX can result in a large speedup [1] in codes that would otherwise not vectorized. For already existing codes it can be 20%.
The best strategy may be to work with ec2 or reject the AVX non-compliant instances.
[1] http://www.behardware.com/medias/photos_news/00/30/IMG003051...