The best compiler for Opteron is still Intel's one, and it will not support AMD64 in any rate. So the 64 bit selling point is rather muted.
I don't see it as a huge problem. You can have both the Intel compiler and the OS supplied compiler (gcc for Linux, MSVC for Windows) installed.
If your application is accessing more than a few Gbytes of data then it will run much faster in a 64 bit version on Opteron than it would in a 32 bit version on a Xeon.
If on the other hand your application doesn't handle large amounts of data then it will also run faster in a 32 bit version (Intel-compiled) on Opteron than it would in a 32 bit version on Xeon.
So either way you win over Xeon, and you likely beat Itanium on price performance by a large margin. Sounds like there will be a market.
The penalty for not using the Intel compiler is at any rate only about 10%. There can be lots of other good reasons for going with the slower compiler apart from 64-bit capability.