Is it possible to run Websphere Application Server 6.1 Test environment in Rational Software Architect (RSA) version 9.0?
I don't mean does it officially support it.. I mean, can you "somehow" get it working in RSA9.
For that you would need a server adapter that you can plug in into RSA. Since RSA is based on eclipse, a server adapter working for eclipse should work for RSA.
Having said that, it is very unlikely (although I do not know for sure) that anyone (in the very least IBM) has provided a publicly available server adapter for WAS 6.1. Usually these are preinstalled with the product and as you already have noticed WAS 6.1 <-> RSA 9.0 is not the best combo. Only supported combinations are preinstalled with IBM products.
It is quite possible to write your own server adapter but since WAS 6.1 is a closed product you may and probably will run into many problems along the way. To get started on writing on your own server adapter you can have a look here. Also some more information about WAS server adapters on eclipse in earlier stackoverflow posts.
Rational licensing is usually not limited to a certain product version, thus you could install and run (provided your licensing allows it) an older version of RSA that supports WAS 6.1 on the same machine where you have your RSA 9 installation.